bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of vitamin D in pulmonary disease: COPD, asthma, infection, and cancer
Authors: Herr Christian , Greulich Timm , Koczulla Rembert A , Meyer Silke , Zakharkina Tetyana , Branscheidt Meret , Eschmann Rebecca , Bals Robert 
Published: March 2011

AbstractThe role of vitamin D (VitD) in calcium and bone homeostasis is well described. In the last years, it has been recognized that in addition to this classical function, VitD modulates a variety of processes and regulatory systems including host defense, inflammation, immunity, and repair. VitD deficiency appears to be frequent in industrialized countries. Especially patients with lung diseases have often low VitD serum levels. Epidemiological data indicate that low levels of serum VitD is associated with impaired pulmonary function, increased incidence of inflammatory, infectious or neoplastic diseases. Several lung diseases, all inflammatory in nature, may be related to activities of VitD including asthma, COPD and cancer. The exact mechanisms underlying these data are unknown, however, VitD appears to impact on the function of inflammatory and structural cells, including dendritic cells, lymphocytes, monocytes, and epithelial cells. This review summarizes the knowledge on the classical and newly discovered functions of VitD, the molecular and cellular mechanism of action and the available data on the relationship between lung disease and VitD status.
MicroSyn: A user friendly tool for detection of microsynteny in a gene family
Authors: Cai Bin , Yang Xiaohan , Tuskan Gerald A , Cheng Zong-Ming 
Published: March 2011

Abstract

Background
The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.

Results
We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: http://fcsb.njau.edu.cn/microsyn/.

Conclusions
Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in Populus trichocarpa were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.
Network based transcription factor analysis of regenerating axolotl limbs
Authors: Jhamb Deepali , Rao Nandini , Milner Derek J , Song Fengyu , Cameron Jo Ann , Stocum David L , Palakal Mathew J 
Published: March 2011

AbstractBackgroundStudies on amphibian limb regeneration began in the early 1700's but we still do not completely understand the cellular and molecular events of this unique process. Understanding a complex biological process such as limb regeneration is more complicated than the knowledge of the individual genes or proteins involved. Here we followed a systems biology approach in an effort to construct the networks and pathways of protein interactions involved in formation of the accumulation blastema in regenerating axolotl limbs.ResultsWe used the human orthologs of proteins previously identified by our research team as bait to identify the transcription factor (TF) pathways and networks that regulate blastema formation in amputated axolotl limbs. The five most connected factors, c-Myc, SP1, HNF4A, ESR1 and p53 regulate ~50% of the proteins in our data. Among these, c-Myc and SP1 regulate 36.2% of the proteins. c-Myc was the most highly connected TF (71 targets). Network analysis showed that TGF-β1 and fibronectin (FN) lead to the activation of these TFs. We found that other TFs known to be involved in epigenetic reprogramming, such as Klf4, Oct4, and Lin28 are also connected to c-Myc and SP1.ConclusionsOur study provides a systems biology approach to how different molecular entities inter-connect with each other during the formation of an accumulation blastema in regenerating axolotl limbs. This approach provides an in silico methodology to identify proteins that are not detected by experimental methods such as proteomics but are potentially important to blastema formation. We found that the TFs, c-Myc and SP1 and their target genes could potentially play a central role in limb regeneration. Systems biology has the potential to map out numerous other pathways that are crucial to blastema formation in regeneration-competent limbs, to compare these to the pathways that characterize regeneration-deficient limbs and finally, to identify stem cell markers in regeneration.
Identification and characterization of maize microRNAs involved in the very early stage of seed germination
Authors: Wang Liwen , Liu Huaihua , Li Detao , Chen Huabang 
Published: March 2011

Abstract
Background
MicroRNAs (miRNAs) are a new class of endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. Extensive studies of miRNAs have been performed in model plants such as rice, Arabidopsis thaliana and other plants. However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the very early stage during seed germination.

Results
In this study, a small RNA library from maize seed 24 hours after imbibition was sequenced by the Solexa technology. A total of 11,338,273 reads were obtained. 1,047,447 total reads representing 431 unique sRNAs matched to known maize miRNAs. Further analysis confirmed the authenticity of 115 known miRNAs belonging to 24 miRNA families and the discovery of 167 novel miRNAs in maize. Both the known and the novel miRNAs were confirmed by sequencing of a second small RNA library constructed the same way as the one used in the first sequencing. We also found 10 miRNAs that had not been reported in maize, but had been reported in other plant species. All novel sequences had not been earlier described in other plant species. In addition, seven miRNA* sequences were also obtained. Putative targets for 106 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in maize imbibed seed.

Conclusions
This study led to the confirmation of the authenticity of 115 known miRNAs and the discovery of 167 novel miRNAs in maize. Identification of novel miRNAs resulted in significant enrichment of the repertoire of maize miRNAs and provided insights into miRNA regulation of genes expressed in imbibed seed.
Herpes simplex virus infections among rural residents in eastern China
Authors: Lin Haijiang , He Na , Su Meifang , Feng Jifu , Chen Li , Gao Meiyang 
Published: March 2011

Abstract

Background
Herpes simplex virus (HSV) has two types: HSV-1 and HSV-2. Both infect epithelial cells and establish latent infections in neurons causing an infection that persists for life. Information on age- and gender-specific seroprevalence of HSV-1 and HSV-2 is valuable for understanding HSV transmission dynamics and designing population-based prevention and intervention programs for HSV. However, such information is not available for China.

Methods
Cryopreserved serum samples of all subjects aged 5 to 60 years from two randomly selected rural villages in Zhejiang province in Eastern China who had participated in the China national seroepidemiological survey of hepatitis B virus (HBV) infection conducted in 2006 were tested. Seroprevalence of HSV-1 and HSV-2 infections were determined by type-specific IgG antibody tests using an ELISA technique. Their 95% confidence intervals adjusted for the sampling fraction were calculated according to the Clopper-Pearson method.

Results
A total of 2,141 residents participated in the survey, with a response rate of 82.3%. HSV-1 seroprevalence was 92.0% overall, 89.1% for males and 94.2% for females. HSV-1 seroprevalence was 61.6% among children aged 5-9 years, 90.3% among 25-29 years, and nearly 100% among those aged > = 40 years. HSV-2 seroprevalence was 13.2% overall, 10.5% for males and 15.3% for females. No children aged 5-14 years were HSV-2 positive, and HSV-2 seroprevalence was 7.1% among 15-19 years and peaked at 24.3% among those aged 45-49 years. Neither HSV-1 nor HSV-2 infections were significantly different by gender. About 11.8% of study subjects were co-infected with both types of HSV. Among 549 participating couples, 8.6% were HSV-1 serodiscordant and 11.8% were HSV-2 serodiscordant. No one tested positive for HIV. The overall prevalence of HBsAg was 16.2%, 16.9% for males and 15.4% for females.

Conclusions
HSV-1 was highly prevalent among all rural residents aged between 5-60 years in Eastern China, whereas HSV-2 was prevalent among sexually active people. HSV-1 and HSV-2 have different transmission modes and dynamics. Future HSV prevention and control programs in China should be type specific.
Theoretical study of the role of metallic contacts in probing transport features of pure and defected graphene nanoribbons
Authors: La Magna Antonino , Deretzis Ioannis 
Published: March 2011

AbstractUnderstanding the roles of disorder and metal/graphene interface on the electronic and transport properties of graphene-based systems is crucial for a consistent analysis of the data deriving from experimental measurements. The present work is devoted to the detailed study of graphene nanoribbon systems by means of self-consistent quantum transport calculations. The computational formalism is based on a coupled Schrödinger/Poisson approach that respects both chemistry and electrostatics, applied to pure/defected graphene nanoribbons (ideally or end-contacted by various fcc metals). We theoretically characterize the formation of metal-graphene junctions as well as the effects of backscattering due to the presence of vacancies and impurities. Our results evidence that disorder can infer significant alterations on the conduction process, giving rise to mobility gaps in the conductance distribution. Moreover, we show the importance of metal-graphene coupling that gives rise to doping-related phenomena and a degradation of conductance quantization characteristics.
Crystallographic plane-orientation dependent atomic force microscopy-based local oxidation of silicon carbide
Authors: Ahn Jung-Joon , Jo Yeong-Deuk , Kim Sang-Cheol , Lee Ji-Hoon , Koo Sang-Mo 
Published: March 2011

AbstractThe effect of crystalline plane orientations of Silicon carbide (SiC) (a-, m-, and c-planes) on the local oxidation on 4H-SiC using atomic force microscopy (AFM) was investigated. It has been found that the AFM-based local oxidation (AFM-LO) rate on SiC is closely correlated to the atomic planar density values of different crystalline planes (a-plane, 7.45 cm-2; c-plane, 12.17 cm-2; and m-plane, 6.44 cm-2). Specifically, at room temperature and under about 40% humidity with a scan speed of 0.5 μm/s, the height of oxides on a- and m-planes 4H-SiC is 6.5 and 13 nm, respectively, whereas the height of oxides on the c-plane increased up to 30 nm. In addition, the results of AFM-LO with thermally grown oxides on the different plane orientations in SiC are compared.
Measurement of the extinction coefficients of magnetic fluids
Authors: Fang Xiaopeng , Xuan Yimin , Li Qiang 
Published: March 2011

AbstractA novel spectral transmittance approach for measuring the extinction coefficient of magnetic fluids is proposed. The measuring principle and accuracy of the approach are analysed. Experiments are conducted to measure the extinction coefficient of magnetic fluids with different particle volume fractions. The relative uncertainty of experimental data is less than 1.8%. The experimental results indicate that the extinction coefficient of magnetic fluids increases with increase of the volume fraction of suspended magnetic nanoparticles and the optical properties of the particle material have a significant effect on the extinction coefficient of the magnetic fluids.
Fast local fragment chaining using sum-of-pair gap costs
Authors: Otto Christian , Hoffmann Steve , Gorodkin Jan , Stadler Peter F 
Published: March 2011

Abstract

Background
Fast seed-based alignment heuristics such as and have become indispensable tools in comparative genomics for all studies aiming at the evolutionary relations of proteins, genes, and non-coding RNAs. This is true in particular for the large mammalian genomes. The sensitivity and specificity of these tools, however, crucially depend on parameters such as seed sizes or maximum expectation values. In settings that require high sensitivity the amount of short local match fragments easily becomes intractable. Then, fragment chaining is a powerful leverage to quickly connect, score, and rank the fragments to improve the specificity.

Results
Here we present a fast and flexible fragment chainer that for the first time also supports a sum-of-pair gap cost model. This model has proven to achieve a higher accuracy and sensitivity in its own field of application. Due to a highly time-efficient index structure our method outperforms the only existing tool for fragment chaining under the linear gap cost model. It can easily be applied to the output generated by alignment tools such as or . As an example we consider homology-based searches for human and mouse snoRNAs demonstrating that a highly sensitive search with subsequent chaining is an attractive option. The sum-of-pair gap costs provide a substantial advantage is this context.

Conclusions
Chaining of short match fragments helps to quickly and accurately identify regions of homology that may not be found using local alignment heuristics alone. By providing both the linear and the sum-of-pair gap cost model, a wider range of application can be covered. The software clasp is available at http://www.bioinf.uni-leipzig.de/Software/clasp/.
Heterogeneity in the kinetics of nuclear proteins and trajectories of substructures associated with heterochromatin
Authors: Stixová Lenka , Bártová Eva , Matula Pavel , Daněk Ondřej , Legartová Soňa , Kozubek Stanislav 
Published: March 2011

AbstractBackgroundProtein exchange kinetics correlate with the level of chromatin condensation and, in many cases, with the level of transcription. We used fluorescence recovery after photobleaching (FRAP) to analyse the kinetics of 18 proteins and determine the relationships between nuclear arrangement, protein molecular weight, global transcription level, and recovery kinetics. In particular, we studied heterochromatin-specific heterochromatin protein 1β (HP1β) B lymphoma Mo-MLV insertion region 1 (BMI1), and telomeric-repeat binding factor 1 (TRF1) proteins, and nucleolus-related proteins, upstream binding factor (UBF) and RNA polymerase I large subunit (RPA194). We considered whether the trajectories and kinetics of particular proteins change in response to histone hyperacetylation by histone deacetylase (HDAC) inhibitors or after suppression of transcription by actinomycin D.ResultsWe show that protein dynamics are influenced by many factors and events, including nuclear pattern and transcription activity. A slower recovery after photobleaching was found when proteins, such as HP1β, BMI1, TRF1, and others accumulated at specific foci. In identical cells, proteins that were evenly dispersed throughout the nucleoplasm recovered more rapidly. Distinct trajectories for HP1β, BMI1, and TRF1 were observed after hyperacetylation or suppression of transcription. The relationship between protein trajectory and transcription level was confirmed for telomeric protein TRF1, but not for HP1β or BMI1 proteins. Moreover, heterogeneity of foci movement was especially observed when we made distinctions between centrally and peripherally positioned foci.ConclusionBased on our results, we propose that protein kinetics are likely influenced by several factors, including chromatin condensation, differentiation, local protein density, protein binding efficiency, and nuclear pattern. These factors and events likely cooperate to dictate the mobility of particular proteins.
Stepped care and cognitive–behavioural therapy for bulimia
nervosa: randomised trial
Authors: Mitchell James E. , Agras Stewart , Crow Scott , Halmi Katherine , Fairburn Christopher G. , Bryson Susan , Kraemer Helena 
Published: March 2011

BackgroundThis study compared the best available treatment for bulimia nervosa,
cognitive–behavioural therapy (CBT) augmented by fluoxetine if indicated,
with a stepped-care treatment approach in order to enhance treatment
effectiveness.AimsTo establish the relative effectiveness of these two approaches.MethodThis was a randomised trial conducted at four clinical centres
(Clinicaltrials.gov registration number: NCT00733525). A total of 293
participants with bulimia nervosa were randomised to one of two treatment
conditions: manual-based CBT delivered in an individual therapy format
involving 20 sessions over 18 weeks and participants who were predicted
to be non-responders after 6 sessions of CBT had fluoxetine added to
treatment; or a stepped-care approach that began with supervised
self-help, with the addition of fluoxetine in participants who were
predicted to be non-responders after six sessions, followed by CBT for
those who failed to achieve abstinence with self-help and medication
management.ResultsBoth in the intent-to-treat and completer samples, there were no
differences between the two treatment conditions in inducing recovery (no
binge eating or purging behaviours for 28 days) or remission (no longer
meeting DSM–IV criteria). At the end of 1-year follow-up, the
stepped-care condition was significantly superior to CBT.ConclusionsTherapist-assisted self-help was an effective first-level treatment in
the stepped-care sequence, and the full sequence was more effective than
CBT suggesting that treatment is enhanced with a more individualised
approach.
Sodium tetradecyl sulphate foam stability prior to injection: factors affecting liquid reformation
Authors: McMaster S 
Published: March 2011

Objective To study the effect of sclerosant concentration, use of 5-µm filter, use of CO2 versus air and needle size on the stability of sodium tetradecyl sulphate (STS) foam and observe the dynamics of liquid reformation from foam within the syringe prior to injection. Method Observations of liquid reformation within the syringe following foam preparation using the Tessari method. Result Foam stability varies little with STS concentration between 0.5% and 3%. Needle size has little effect in this study. An in-line filter produces significantly more stable foam, and CO2 foam is significantly less stable than air foam. Liquid reformation is predictable and does not progress at a constant rate. Conclusion Regardless of the method and details of the foam produced, sclerotherapists should be aware of the dynamics and speed of foam degradation, and reconstitute foam at the first sign of liquid reformation, as this heralds the onset of rapid degradation of the foam. This is particularly relevant for rapidly deteriorating foam produced from CO2, or without the use of a filter.
Whole Blood Immunoassay Based on Centrifugal Bead Sedimentation
Authors: Schaff Ulrich Y , Sommer Greg J 
Published: March 2011

BACKGROUND
Centrifugal “lab on a disk” microfluidics is a promising avenue for developing portable, low-cost, automated immunoassays. However, the necessity of incorporating multiple wash steps results in complicated designs that increase the time and sample/reagent volumes needed to run assays and raises the probability of errors. We present proof of principle for a disk-based microfluidic immunoassay technique that processes blood samples without conventional wash steps.

METHODS
Microfluidic disks were fabricated from layers of patterned, double-sided tape and polymer sheets. Sample was mixed on-disk with assay capture beads and labeling antibodies. Following incubation, the assay beads were physically separated from the blood cells, plasma, and unbound label by centrifugation through a density medium. A signal-laden pellet formed at the periphery of the disk was analyzed to quantify concentration of the target analyte.

RESULTS
To demonstrate this technique, the inflammation biomarkers C-reactive protein and interleukin-6 were measured from spiked mouse plasma and human whole blood samples. On-disk processing (mixing, labeling, and separation) facilitated direct assays on 1-μL samples with a 15-min sample-to-answer time, &lt;100 pmol/L limit of detection, and 10% CV. We also used a unique single-channel multiplexing technique based on the sedimentation rate of different size or density bead populations.

CONCLUSIONS
This portable microfluidic system is a promising method for rapid, inexpensive, and automated detection of multiple analytes directly from a drop of blood in a point-of-care setting.
Pilot Evaluation for Lead-Based Paint Proficiency Testing of Field Portable XRF Instruments
Authors: White Kenneth T. , Dewalt F. Gary , Cox David C. , Schmehl Richard , Friedman Warren , Pinzer Eugene A. 
Published: March 2011

Abstract
A proficiency testing procedure for evaluating the accuracy of lead measurements taken by certified lead-based paint inspectors using portable X-ray fluorescence (XRF) instruments was developed and pilot tested. XRF instruments are widely used for inspection of housing units to determine the presence or absence of lead-based paint. Previous research showed variability between different XRF instruments when used to conduct lead-based paint inspections. Due to concerns over potential errors in inspection reports resulting from biased XRF measurements, a proficiency testing procedure was pilot tested to provide entities, such a state or federal regulators, a means of evaluating the instrumentation being used for lead-based paint inspections.