bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photic EEG-driving responses related to ictal phases and trigger sensitivity in migraine: A longitudinal, controlled study
Authors: Bjørk M , Hagen K , Stovner Lj , Sand T 
Published: November 2010

Introduction Photic driving is believed to be increased in migraineurs and has been interpreted as a sign of cortical hyperexcitability. However, most previous studies have included patients in various phases of the migraine cycle. The results are, therefore, difficult to interpret as neurophysiological abnormalities tend to accumulate close to the attack in migraineurs. Subjects and Methods We recorded steady state visual evoked EEG-responses (SSVEPs) for 6, 12, 18 and 24 Hz flash stimuli from 33 migraineurs without aura, eight migraineurs with aura and 32 healthy controls. Interictal recordings were compared pair-wise with recordings before, during and after attack, as well as with EEGs from healthy controls. Driving power was also correlated with sensory hypersensitivity and severity of migraine. Results Between attacks, driving responses to 18 Hz and 24 Hz were attenuated in migraineurs without aura. Driving power of 12 Hz increased before the attack. Attack trigger sensitivity, photophobia, pain intensity and a family history of migraine were related to decreased and/or symmetric photic driving. Conclusions Earlier results may have overestimated the driving response in migraine due to inclusion of recordings during the preictal interval and/or habituation among controls. Abnormal photic driving may be related to the pathophysiology of clinical sensory hypersensitivity.
Peptide binding predictions for HLA DR, DP and DQ molecules
Authors: Wang Peng , Sidney John , Kim Yohan , Sette Alessandro , Lund Ole , Nielsen Morten , Peters Bjoern 
Published: November 2010

AbstractBackgroundMHC class II binding predictions are widely used to identify epitope candidates in infectious agents, allergens, cancer and autoantigens. The vast majority of prediction algorithms for human MHC class II to date have targeted HLA molecules encoded in the DR locus. This reflects a significant gap in knowledge as HLA DP and DQ molecules are presumably equally important, and have only been studied less because they are more difficult to handle experimentally.ResultsIn this study, we aimed to narrow this gap by providing a large scale dataset of over 17,000 HLA-peptide binding affinities for a set of 11 HLA DP and DQ alleles. We also expanded our dataset for HLA DR alleles resulting in a total of 40,000 MHC class II binding affinities covering 26 allelic variants. Utilizing this dataset, we generated prediction tools utilizing several machine learning algorithms and evaluated their performance.ConclusionWe found that 1) prediction methodologies developed for HLA DR molecules perform equally well for DP or DQ molecules. 2) Prediction performances were significantly increased compared to previous reports due to the larger amounts of training data available. 3) The presence of homologous peptides between training and testing datasets should be avoided to give real-world estimates of prediction performance metrics, but the relative ranking of different predictors is largely unaffected by the presence of homologous peptides, and predictors intended for end-user applications should include all training data for maximum performance. 4) The recently developed NN-align prediction method significantly outperformed all other algorithms, including a naïve consensus based on all prediction methods. A new consensus method dropping the comparably weak ARB prediction method could outperform the NN-align method, but further research into how to best combine MHC class II binding predictions is required.
Reticular alignment: A progressive corner-cutting method for multiple sequence alignment
Authors: Szabó Adrienn , Novák Ádám , Miklós István , Hein Jotun 
Published: November 2010

Abstract

Background
In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead, it defines a set of optimal and suboptimal alignments at each step during the progressive alignment. The set of alignments are represented with a network to store them and use them during the progressive alignment in an efficient way. The program contains a threshold parameter on which the size of the network depends. The larger the threshold parameter and thus the network, the deeper the search in the alignment space for better scored alignments.

Results
We implemented the program in the Java programming language, and tested it on the BAliBASE database. Reticular Alignment can outperform ClustalW even if a very simple scoring scheme (BLOSUM62 and affine gap penalty) is implemented and merely the threshold value is increased. However, this set-up is not sufficient for outperforming other cutting-edge alignment methods. On the other hand, the reticular alignment search strategy together with sophisticated scoring schemes (for example, differentiating gap penalties for hydrophobic and hydrophylic amino acids) overcome FSA and in some accuracy measurement, even MAFFT. The program is available from http://phylogeny-cafe.elte.hu/RetAlign/

Conclusions
Reticular alignment is an efficient search strategy for finding accurate multiple alignments. The highest accuracy achieved when this searching strategy is combined with sophisticated scoring schemes.
Comparative genomic analysis of Atlantic salmon, Salmo salar, from Europe and North America
Authors: Lubieniecki Krzysztof P , Jones Stacy L , Davidson Evelyn A , Park Jay , Koop Ben F , Walker Seumas , Davidson William S 
Published: November 2010

Abstract

Background
Several lines of evidence including allozyme analysis, restriction digest patterns and sequencing of mtDNA as well as mini- and micro-satellite allele frequencies indicate that Atlantic salmon (Salmo salar) from North America and Europe are genetically distinct. These observations are supported by karyotype analysis, which revealed that North American Atlantic salmon have 27 pairs of chromosomes whereas European salmon have 29 pairs. We set out to construct a linkage map for a North American Atlantic salmon family and to compare this map with the well developed map for European Atlantic salmon.

Results
We used microsatellite markers, which had previously been mapped in the two Atlantic salmon SALMAP mapping families from the River Tay, Scotland, to carry out linkage analysis in an Atlantic salmon family (NB1) whose parents were derived from the Saint John River stock in New Brunswick, Canada. As large differences in recombination rates between female and male Atlantic salmon have been noted, separate genetic maps were constructed for each sex. The female linkage map comprises 218 markers in 37 linkage groups while the male map has 226 markers in 28 linkage groups. We combined 280 markers from the female and male maps into 27 composite linkage groups, which correspond to the haploid number of chromosomes in Atlantic salmon from the Western Atlantic.

Conclusions
A comparison of the composite NB1 and SALMAP linkage maps revealed the reason for the difference in the chromosome numbers between European and North American Atlantic salmon: Linkage groups AS-4 and AS-32 in the Scottish salmon, which correspond to chromosomes Ssa-6 and Ssa-22, are combined into a single NB1 linkage group as are linkage groups AS-21 and AS-33 (corresponding to chromosomes Ssa-26 and Ssa-28). The comparison of the linkage maps also suggested some additional chromosomal rearrangements, but it will require finer mapping, potentially using SNPs, to test these predictions. Our results provide the first comparison of the genomic architecture of Atlantic salmon from North America and Europe with respect to chromosome organization.
Identification and analysis of the germin-like gene family in soybean
Authors: Lu Mo , Han Ying-Peng , Gao Ji-Guo , Wang Xiang-Jing , Li Wen-Bin 
Published: November 2010

Abstract

Background
Germin and germin-like proteins constitute a ubiquitous family of plant proteins. A role of some family members in defense against pathogen attack had been proposed based on gene regulation studies and transgenic approaches. Soybean (G. max L. Merr.) germin genes had not been characterized at the molecular and functional levels.

Results
In the present study, twenty-one germin gene members in soybean cultivar 'Maple Arrow' (partial resistance to Sclerotinia stem rot of soybean) were identified by in silico identification and RACE method (GmGER 1 to GmGER 21). A genome-wide analyses of these germin-like protein genes using a bioinformatics approach showed that the genes located on chromosomes 8, 1, 15, 20, 16, 19, 7, 3 and 10, on which more disease-resistant genes were located on. Sequence comparison revealed that the genes encoded three germin-like domains. The phylogenetic relationships and functional diversity of the germin gene family of soybean were analyzed among diverse genera. The expression of the GmGER genes treated with exogenous IAA suggested that GmGER genes might be regulated by auxin. Transgenic tobacco that expressed the GmGER 9 gene exhibited high tolerance to the salt stress. In addition, the GmGER mRNA increased transiently at darkness and peaked at a time that corresponded approximately to the critical night length. The mRNA did not accumulate significantly under the constant light condition, and did not change greatly under the SD and LD treatments.

Conclusions
This study provides a complex overview of the GmGER genes in soybean. Phylogenetic analysis suggested that the germin and germin-like genes of the plant species that had been founded might be evolved by independent gene duplication events. The experiment indicated that germin genes exhibited diverse expression patterns during soybean development. The different time courses of the mRNAs accumulation of GmGER genes in soybean leaves appeared to have a regular photoperiodic reaction in darkness. Also the GmGER genes were proved to response to abiotic stress (such as auxin and salt), suggesting that these paralogous genes were likely involved in complex biological processes in soybean.
Expression of 3-hydroxy-3-methylglutaryl-CoA reductase, p-hydroxybenzoate-m-geranyltransferase and genes of phenylpropanoid pathway exhibits positive correlation with shikonins content in arnebia [Arnebia euchroma (Royle) Johnston]
Authors: Singh Ravi S , Gara Rishi K , Bhardwaj Pardeep K , Kaachra Anish , Malik Sonia , Kumar Ravi , Sharma Madhu , Ahuja Paramvir S , Kumar Sanjay 
Published: November 2010

Abstract

Background
Geranyl pyrophosphate (GPP) and p-hydroxybenzoate (PHB) are the basic precursors involved in shikonins biosynthesis. GPP is derived from mevalonate (MVA) and/or 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway(s), depending upon the metabolite and the plant system under consideration. PHB, however, is synthesized by only phenylpropanoid (PP) pathway. GPP and PHB are central moieties to yield shikonins through the synthesis of m-geranyl-p-hydroxybenzoate (GHB). Enzyme p-hydroxybenzoate-m-geranyltransferase (PGT) catalyses the coupling of GPP and PHB to yield GHB.
The present research was carried out in shikonins yielding plant arnebia [Arnebia euchroma (Royle) Johnston], wherein no molecular work has been reported so far. The objective of the work was to identify the preferred GPP synthesizing pathway for shikonins biosynthesis, and to determine the regulatory genes involved in the biosynthesis of GPP, PHB and GHB.

Results
A cell suspension culture-based, low and high shikonins production systems were developed to facilitate pathway identification and finding the regulatory gene. Studies with mevinolin and fosmidomycin, inhibitors of MVA and MEP pathway, respectively suggested MVA as a preferred route of GPP supply for shikonins biosynthesis in arnebia. Accordingly, genes of MVA pathway (eight genes), PP pathway (three genes), and GHB biosynthesis were cloned. Expression studies showed down-regulation of all the genes in response to mevinolin treatment, whereas gene expression was not influenced by fosmidomycin. Expression of all the twelve genes vis-à-vis shikonins content in low and high shikonins production system, over a period of twelve days at frequent intervals, identified critical genes of shikonins biosynthesis in arnebia.

Conclusion
A positive correlation between shikonins content and expression of 3-hydroxy-3-methylglutaryl-CoA reductase (AeHMGR) and AePGT suggested critical role played by these genes in shikonins biosynthesis. Higher expression of genes of PP pathway was a general feature for higher shikonins biosynthesis.
Subcellular distribution of nuclear import-defective isoforms of the promyelocytic leukemia protein
Authors: Jul-Larsen Åsne , Grudic Amra , Bjerkvig Rolf , Bøe Stig O 
Published: November 2010

Abstract

Background
The promyelocytic leukemia (PML) protein participates in a number of cellular processes, including transcription regulation, apoptosis, differentiation, virus defense and genome maintenance. This protein is structurally organized into a tripartite motif (TRIM) at its N-terminus, a nuclear localization signal (NLS) at its central region and a C-terminus that varies between alternatively spliced isoforms. Most PML splice variants target the nucleus where they define sub-nuclear compartments termed PML nuclear bodies (PML NBs). However, PML variants that lack the NLS are also expressed, suggesting the existence of PML isoforms with cytoplasmic functions. In the present study we expressed PML isoforms with a mutated NLS in U2OS cells to identify potential cytoplasmic compartments targeted by this protein.

Results
Expression of NLS mutated PML isoforms in U2OS cells revealed that PML I targets early endosomes, PML II targets the inner nuclear membrane (partially due to an extra NLS at its C-terminus), and PML III, IV and V target late endosomes/lysosomes. Clustering of PML at all of these subcellular locations depended on a functional TRIM domain.

Conclusions
This study demonstrates the capacity of PML to form macromolecular protein assemblies at several different subcellular sites. Further, it emphasizes a role of the variable C-terminus in subcellular target selection and a general role of the N-terminal TRIM domain in promoting protein clustering.
IP-10 detection in urine is associated with lung diseases
Authors: Cannas Angela , Calvo Ludovica , Chiacchio Teresa , Cuzzi Gilda , Vanini Valentina , Lauria Francesco N , Pucci Luigia , Girardi Enrico , Goletti Delia 
Published: November 2010

AbstractBackgroundblood cytokines and chemokines have been proposed as biomarkers for tuberculosis (TB). Recently, some immune mediators found in the urine of patients with renal dysfunctions have also been suggested as potential biomarkers. Finding biomarkers for TB in urine would present several advantages over blood in terms of collection and safety. The objective of this study was to investigate the presence of cytokines and chemokines in the urine of patients with pulmonary TB at the time of diagnosis. In a subgroup, the evaluation was also performed during TB treatment and at therapy completion. Patients with lung diseases other than TB, and healthy subjects were also enrolled.Methodsurine samples from 138 individuals, after exclusion of renal dysfunctions, were collected during an 18 month-period. Among them, 58 received a diagnosis of pulmonary TB, 28 resulted having lung diseases other than TB, and 34 were healthy subjects. Moreover, 18 TB patients, 9 of whom were tested 2 months after AFB smear sputum reversion and 9 of whom were cured of TB were also included. Cytokines and chemokines in urine were evaluated using a Cytometric-Bead-Array-Flex-Set. IP-10 detection in 49 subjects was also carried out in parallel by using an Enzyme Linked ImmunoSorbent Assay (ELISA).ResultsIFN-γ, TNF-α, IL-2, IL-8, MIP-1α, MIP-1β and RANTES were poorly detected in all urine samples. Conversely, IP-10 was consistently detected in urine and its level was significantly increased in patients with lung disease compared to healthy subjects (p < 0.001). Increased IP-10 levels were found in both pulmonary TB and lung diseases other than TB. Moreover lower IP-10 levels were found in cured-TB patients compared to the levels at the time of diagnosis, and this difference was close to significance (p = 0.06). Interestingly, we demonstrated a significant correlation between the data obtained by flow cytometry and ELISA (r20.82, p < 0.0001).ConclusionsIP-10, in contrast to IFN-γ, TNF-α, IL-2, IL-8, MIP-1α, MIP-1β and RANTES, is detectable in the urine of patients with pulmonary diseases in the absence of renal dysfunctions. Moreover, the IP-10 level in cured-TB patients is comparable to that found in healthy subjects. More studies are needed to further investigate the clinical utility of these findings.
Prevalence and clustering of metabolic risk factors for type 2 diabetes among Chinese adults in Shanghai, China
Authors: Xu He , Song Yiqing , You Nai-Chieh , Zhang Zuo-Feng , Greenland Sander , Ford Earl S , He Lin , Liu Simin 
Published: November 2010

Abstract

Background
Type 2 diabetes is becoming an epidemic in China. To evaluate the prevalence, clustering of metabolic risk factors and their impact on type 2 diabetes, we conducted a population-based study in Shanghai, China's largest metropolitan area.

Methods
From 2006 to 2007, 2,113 type 2 diabetes cases and 2,458 comparable controls of adults aged 40 to 79 years were enrolled. Demographic, lifestyle, and dietary factors were assessed via standardized questionnaires. Plasma, red and white blood cells were collected and stored for future studies. Anthropometric indices and biochemical intermediates (including blood pressure, fasting glucose, glycosylated hemoglobin, and blood lipids) were measured. The prevalence of metabolic syndrome were also compared following two criteria recommended by the Chinese Diabetes Society (CDS, 2004) and the National Cholesterol Education Program's Adult Treatment Panel III (ATP III, 2002).

Results
Prevalence of metabolic syndrome (62% vs. 15% using CDS criteria) and its individual components, including obesity (51% vs. 42%), hypertension (54% vs. 41%), hypertriglyceridemia (42% vs. 32%), and low high-density lipoprotein-cholesterol (HDL) levels (36% vs. 25%) were higher in diabetes cases than controls. Regardless of criteria used, those with impaired fasting glucose (IFG) had similarly high prevalence of metabolic syndrome as did diabetes cases. In a multiple logistic regression model adjusted for demographics and lifestyle risk factors, the odds ratios of diabetes (95% CI) were 1.23 (1.04-1.45) for overweight (28 >= BMI >= 24), 1.81 (1.45-2.25) for obesity (BMI > 28), 1.53 (1.30-1.80) for central obesity (waist circumference > 80 cm for woman or waist circumference > 85 cm for man), 1.36 (1.17-1.59) for hypertension (sbp/dbp >= 140/90 mmHg), 1.55 (1.32-1.82) for high triglycerides (triglycerides > 1.70 mmol/l) and 1.52 (1.23-1.79) for low HDL-C (HDL-C < 1.04 mmol/L).

Conclusions
These data indicate that multiple metabolic risk factors--individually or jointly--were more prevalent in diabetes patients than in controls. Further research will examine hypotheses concerning the high prevalence of IFG, family history, and central obesity, aiding development of multifaceted preventive strategies specific to this population.
Rationale and methods of the cardiometabolic valencian study (escarval-risk) for validation of risk scales in mediterranean patients with hypertension, diabetes or dyslipidemia
Authors: Gil-Guillen Vicente , Orozco-Beltran Domingo , Redon Josep , Pita-Fernandez Salvador , Navarro-Pérez Jorge , Pallares Vicente , Valls Francisco , Fluixa Carlos , Fernandez Antonio , Martin-Moreno Jose M , Pascual-de-la-Torre Manuel , Trillo Jose L , Durazo-Arvizu Ramon , Cooper Richard , Hermenegildo Marta , Rosado Luis 
Published: November 2010

Abstract

Background
The Escarval-Risk study aims to validate cardiovascular risk scales in patients with hypertension, diabetes or dyslipidemia living in the Valencia Community, a European Mediterranean region, based on data from an electronic health recording system comparing predicted events with observed during 5 years follow-up study.

Methods/Design
A cohort prospective 5 years follow-up study has been designed including 25000 patients with hypertension, diabetes and/or dyslipidemia attended in usual clinical practice. All information is registered in a unique electronic health recording system (ABUCASIS) that is the usual way to register clinical practice in the Valencian Health System (primary and secondary care). The system covers about 95% of population (near 5 million people). The system is linked with database of mortality register, hospital withdrawals, prescriptions and assurance databases in which each individual have a unique identification number. Diagnoses in clinical practice are always registered based on IDC-9. Occurrence of CV disease was the main outcomes of interest. Risk survival analysis methods will be applied to estimate the cumulative incidence of developing CV events over time.

Discussion
The Escarval-Risk study will provide information to validate different cardiovascular risk scales in patients with hypertension, diabetes or dyslipidemia from a low risk Mediterranean Region, the Valencia Community.
Initial experience of transumbilical laparoendoscopic single-site surgery of partial adrenalectomy in patient with aldosterone-producing adenoma
Authors: Yuge Kazuyuki , Miyajima Akira , Hasegawa Masanori , Miyazaki Yasumasa , Maeda Takahiro , Takeda Toshikazu , Takeda Ayano , Miyashita Kazutoshi , Kurihara Isao , Shibata Hirotaka , Kikuchi Eiji , Oya Mototsugu 
Published: November 2010

Abstract

Background
Laparoscopic single-site surgery has recently emerged in the field of urology and this minimally-invasive surgery has resulted in a further reduction in morbidity compared with traditional laparoscopy. We present our initial experience with laparoendoscopic single-site surgery of partial adrenalectomy (LESS-PA) to treat aldosterone-producing adenomas.

Case presentation
A 60-year-old woman was diagnosed with aldosterone-producing macroadenomas in the left adrenal and aldosterone-producing microadenomas in the right adrenal. A two-step operation was planned. The first step involved transumbilical LESS-PA for the left adrenal tumors. A multichannel port was inserted through the center of the umbilicus and the left adrenal gland was approached using bent instruments according to standard traditional laparoscopic procedures. The tumors were resected using an ultrasonic scalpel, and the resected site was coagulated using a vessel sealing instrument and then sealed with fibrin glue. Operative time was 123 minutes and blood loss was minimal. The patient was discharged from hospital within 72 hours. Her right adrenal microadenomas will be treated in the next several months.

Conclusions
Although our experience is limited, LESS-PA appears to be safe and feasible for treating aldosterone-producing adenomas. More cases and comparisons with the multiport technique are needed before drawing any definite conclusions concerning the technique.