bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABrowse - a customizable next-generation genome browser framework
Authors: Kong Lei , Wang Jun , Zhao Shuqi , Gu Xiaocheng , Luo Jingchu , Gao Ge 
Published: January 2012

Abstract

Background
With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects.

Results
Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access.

Conclusions
ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.
Actinobaculum schaalii- invasive pathogen or innocent bystander? A retrospective observational study
Authors: Tschudin-Sutter Sarah , Frei Reno , Weisser Maja , Goldenberger Daniel , Widmer Andreas F 
Published: January 2012

Abstract

Background

Actinobaculum schaalii is a Gram-positive, facultative anaerobic coccoid rod, classified as a new genus in 1997. It grows slowly and therefore is easily overgrown by other pathogens, which are often found concomitantly. Since 1999, Actinobaculum schaalii is routinely investigated at our hospital, whenever its presence is suspected due to the detection of minute grey colonies on blood agar plates and negative reactions for catalase. The objective of this study was to determine the clinical significance of Actinobaculum schaalii, identified in our microbiology laboratory over the last 11 years.

Methods
All consecutive isolates with Actinobaculum schaalii were obtained from the computerized database of the clinical microbiology laboratory and patients whose cultures from any body site yielded this pathogen were analyzed. Observation of tiny colonies of Gram-positive, catalase-negative coccoid rods triggered molecular identification based on 16S rRNA gene sequencing.

Results
40 isolates were obtained from 27 patients during the last 11 years. The patient's median age was 81 (19-101) years, 25 (92.6%) had underlying diseases and 12 (44.4%) had a genitourinary tract pathology. Actinobaculum schaalii was isolated in 12 urine cultures, 21 blood cultures, and 7 deep tissue biopsies. Twenty-five (62.5%) specimens were monobacterial, the remaining 15 (37.5%) were polybacterial 7/7 deep tissue samples (three bloodcultures and five urine cultures). Recovery from urine was interpreted as colonization in 5 (18.6%) cases (41.6% of all urine samples). Six (22.2%) suffered from urinary tract infections, six (22.2%) from abscesses (skin, intraabdominal, genitourinary tract, and surgical site infections) and 10 (37.0%) from bacteremia.

Conclusions
In this largest case series so far, detection of Actinobaculum schaalii was associated with an infection - primarily sepsis and abscesses - in 81.5% of our patients. Since this pathogen is frequently part of polymicrobial cultures (42.5%) it is often overlooked or considered a contaminant. Detection of Actinobaculum schaalii in clinical isolates mainly reflects infection indicating that this Gram-positive rod is not an innocent bystander.
Construction of permanently inducible miRNA-based expression vectors using site-specific recombinases
Authors: Garwick-Coppens Sara E , Herman Adam , Harper Scott Q 
Published: January 2012

Abstract

Background
RNA interference (RNAi) is a conserved gene silencing mechanism mediated by small inhibitory microRNAs (miRNAs).
Promoter-driven miRNA expression vectors have emerged as important tools for delivering natural or artificially designed miRNAs to eukaryotic cells and organisms. Such systems can be used to query the normal or pathogenic functions of natural miRNAs or messenger RNAs, or to therapeutically silence disease genes.

Results
As with any molecular cloning procedure, building miRNA-based expression constructs requires a time investment and some molecular biology skills. To improve efficiency and accelerate the construction process, we developed a method to rapidly generate miRNA expression vectors using recombinases instead of more traditional cut-and-paste molecular cloning techniques. In addition to streamlining the construction process, our cloning strategy provides vectors with added versatility. In our system, miRNAs can be constitutively expressed from the U6 promoter, or inducibly expressed by Cre recombinase. We also engineered a built-in mechanism to destroy the vector with Flp recombinase, if desired. Finally, to further simplify the construction process, we developed a software package that automates the prediction and design of optimal miRNA sequences using our system.

Conclusions
We designed and tested a modular system to rapidly clone miRNA expression cassettes. Our strategy reduces the hands-on time required to successfully generate effective constructs, and can be implemented in labs with minimal molecular cloning expertise. This versatile system provides options that permit constitutive or inducible miRNA expression, depending upon the needs of the end user. As such, it has utility for basic or translational applications.
Palmitic and linoleic acids induce ER stress and apoptosis in hepatoma cells
Authors: Zhang Yong , Xue Rongliang , Zhang Zhenni , Yang Xia , Shi Hongyang 
Published: January 2012

Abstract

Objectives
Hepatic inflammation and degeneration induced by lipid depositions may be the major cause of nonalcoholic fatty liver disease. In this study, we tried to investigate the effects of saturated and unsaturated fatty acids on hepatoma cell apoptosis.

Methods
H4IIE liver cells were treated with palmitic acid, linoleic acid, or both with or without the calcium-specific chelator BAPTA-AM after which the expression of proteins associated with endoplasmic reticulum (ER) stress, apoptosis, caspase-3 levels, and calcium flux were measured.

Results
Palmitic or linoleic acid (250 μM) induced H4IIE cell apoptosis, which required calcium flux but not caspase-3. Apoptosis was not observed when cells were co-treated with linoleic acid (125 μM) and palmitic acid (250 μM). Importantly, the release of cytochrome C from mitochondria into cytoplasm during cell apoptosis was specifically detected only when linoleic acid (125 μM), but not palmitic acid (250 μM), was added to the cells. Depletion of intracellular calcium flux by the calcium-specific chelator, BAPTA-AM, abolished linoleic acid-induced apoptosis. Moreover, in the presence of BAPTA-AM, expression of the unfolded protein response (UPR)-associated genes, CHOP, GRP78, and GRP94, was induced by linoleic acid, but not palmitic acid.

Conclusions
The results suggest that linoleic acid promotes cell apoptosis through the release of cytochrome C, only if the intracellular calcium flux is unperturbed and intact. These results confirm that ER stress contributes to fatty acid-induced liver cell apoptosis.
5-Azacytidine Is Insufficient For Cardiogenesis In Human Adipose-Derived Stem Cells
Authors: Wan Safwani Wan Kamarul Zaman , Makpol Suzana , Sathapan Somasundaram , Chua Kien Hui 
Published: January 2012

Abstract

Background
Adipose tissue is a source of multipotent adult stem cells and it has the ability to differentiate into several types of cell lineages such as neuron cells, osteogenic cells and adipogenic cells. Several reports have shown adipose-derived stem cells (ASCs) have the ability to undergo cardiomyogenesis. Studies have shown 5-azacytidine can successfully drive stem cells such as bone marrow derived stem cells to differentiate into cardiomyogenic cells. Therefore, in this study, we investigated the effect 5-azacytidine on the cardiogenic ability of ASCs.

Methods
The cardiogenic potential of ASCs was analysed by studying the morphological changes after induction, the changes in the cardiogenic genes expression i.e. GATA4, MLC-2v, MLC-2a, NKX2.5, β-MHC, α-MHC, Atrial natriuretic peptide (ANP), Connexin 43, Cardiac Troponin C, Cardiac Troponin I and myocyte enhancer factor (MEF2C) and the changes of embryonic stem cells genes expression at P5 and P10 using quantitative PCR.

Results
Our results showed that the induced ASCs did not show significant morphological difference compared to the non-induced ASCs. While quantitative PCR data indicated that most cardiogenic genes and stemness genes expression level decreased after induction at P5 and P10.

Conclusion
5-azacytidine is insufficient for the cardiogenic induction of the ASCs.
Effects of adjuvants on IgG subclasses elicited by virus-like Particles
Authors: Visciano Maria Luisa , Tagliamonte Maria , Tornesello Maria Lina , Buonaguro Franco M , Buonaguro Luigi 
Published: January 2012

AbstractBackgroundVirus-Like Particles (VLPs) represent an efficient strategy to present and deliver conformational antigens to the immune system, inducing both arms of the adaptive immune response. Moreover, their particulate structure surrounded by cell membrane provides an adjuvanted effect to VLP-based immunizations. In the present study, the elicitation of different patterns of IgG subclasses by VLPs, administered in CpG ODN1826 or poly(I:C) adjuvants, has been evaluated in an animal model.ResultsAdjuvanted VLPs elicited a higher titer of total specific IgG compared to VLPs alone. Furthermore, while VLPs alone induced a balanced TH2 pattern, VLPs formulated with either adjuvant elicited a TH1-biased IgG subclasses (IgG2a and IgG3), with poly(I:C) more potent than CpG ODN1826.ConclusionsThe results confirmed that adjuvants efficiently improve antigen immunogenicity and represent a suitable strategy to skew the adaptive immune response toward the differentiation of the desired T helper subset, also using VLPs as antigen.
Polystyrene-Al2O3 composite solid polymer electrolyte for lithium secondary battery
Authors: Lim Yu-Jeong , An Yu-Ha , Jo Nam-Ju 
Published: January 2012

Abstract
In a common salt-in-polymer electrolyte, a polymer which has polar groups in the molecular chain is necessary because the polar groups dissolve lithium salt and coordinate cations. Based on the above point of view, polystyrene [PS] that has nonpolar groups is not suitable for the polymer matrix. However, in this PS-based composite polymer-in-salt system, the transport of cations is not by segmental motion but by ion-hopping through a lithium percolation path made of high content lithium salt. Moreover, Al2O3 can dissolve salt, instead of polar groups of polymer matrix, by the Lewis acid-base interactions between the surface group of Al2O3 and salt. Notably, the maximum enhancement of ionic conductivity is found in acidic Al2O3 compared with neutral and basic Al2O3 arising from the increase of free ion fraction by dissociation of salt. It was revealed that PS-Al2O3 composite solid polymer electrolyte containing 70 wt.% salt and 10 wt.% acidic Al2O3 showed the highest ionic conductivity of 9.78 × 10-5 Scm-1 at room temperature.
Structural and optical properties of ZnS thin films deposited by RF magnetron sputtering
Authors: Hwang Dong Hyun , Ahn Jung Hoon , Hui Kwun Nam , Hui Kwan San , Son Young Guk 
Published: January 2012

Abstract
Zinc sulfide [ZnS] thin films were deposited on glass substrates using radio frequency magnetron sputtering. The substrate temperature was varied in the range of 100°C to 400°C. The structural and optical properties of ZnS thin films were characterized with X-ray diffraction [XRD], field emission scanning electron microscopy [FESEM], energy dispersive analysis of X-rays and UV-visible transmission spectra. The XRD analyses indicate that ZnS films have zinc blende structures with (111) preferential orientation, whereas the diffraction patterns sharpen with the increase in substrate temperatures. The FESEM data also reveal that the films have nano-size grains with a grain size of approximately 69 nm. The films grown at 350°C exhibit a relatively high transmittance of 80% in the visible region, with an energy band gap of 3.79 eV. These results show that ZnS films are suitable for use as the buffer layer of the Cu(In, Ga)Se2 solar cells.
Carbon-coated iron oxide nanoparticles as contrast agents in magnetic resonance imaging
Authors: Bae Hongsub , Ahmad Tanveer , Rhee Ilsu , Chang Yongmin , Jin Seong-Uk , Hong Sungwook 
Published: January 2012

Abstract
Coprecipitated ferrite nanoparticles were coated with carbon using a hydrothermal method. From transmission electron microscope pictures, we could see that the coated iron oxide nanoparticles were spherical in shape with an average diameter of 90 nm. The strong bonding of carbon on the nanoparticle surfaces was checked by noting the C = O and C = C vibrations in Fourier transform infrared spectra. The spin-lattice relaxation process [T
1] and spin-spin relaxation process [T
2] relaxivities of hydrogen protons in the aqueous solution of coated nanoparticles were determined to be 1.139 (mM·s)-1 and 1.115 (mM·s)-1, respectively. These results showed that the carbon-coated iron oxide nanoparticles are applicable as both T
1 and T
2 contrast agents in magnetic resonance imaging.

PACS: 81.05.y; 76.60.Es; 61.46; 75.50.k; 87.61.
Influences of phase transition and microstructure on dielectric properties of Bi0.5Na0.5Zr1-xTixO3 ceramics
Authors: Jaiban Panupong , Rachakom Ampika , Jiansirisomboon Sukanda , Watcharapasorn Anucha 
Published: January 2012

Abstract
Bismuth sodium zirconate titanate ceramics with the formula Bi0.5Na0.5Zr1-xTixO3 [BNZT], where x = 0.3, 0.4, 0.5, and 0.6, were prepared by a conventional solid-state sintering method. Phase identification was investigated using an X-ray diffraction technique. All compositions exhibited complete solubility of Ti4+ at the Zr4+ site. Both a decrease of unit cell size and phase transition from an orthorhombic Zr-rich composition to a rhombohedral crystal structure in a Ti-rich composition were observed as a result of Ti4+ substitution. These changes caused dielectric properties of BNZT ceramics to enhance. Microstructural observation carried out employing SEM showed that average grain size decreased when addition of Ti increased. Grain size difference of BNZT above 0.4 mole fraction of Ti4+ displayed a significant increase of dielectric constant at room temperature.
Effects of ZnO nanoparticulate addition on the properties of PMNT ceramics
Authors: Promsawat Methee , Watcharapasorn Anucha , Jiansirisomboon Sukanda 
Published: January 2012

Abstract
This research was conducted in order to study the effect of ZnO nanoparticulate addition on the properties of 0.9 Pb(Mg1/3Nb2/3)O3-0.1PbTiO3 [PMNT] ceramics. The PMNT ceramics were prepared by a solid-state reaction. The ZnO nanoparticles were added into PMNT ceramics to form PMNT/x ZnO (x = 0, 0.05, 0.1, 0.5, and 1.0 wt.%). The PMNT/x ZnO ceramics were investigated in terms of phase, microstructure, and mechanical and electrical properties. It was found that the density and grain size of PMNT ceramics tended to increase with an increasing amount of ZnO content. Moreover, a transgranular fracture was observed for the samples containing ZnO, while pure PMNT ceramics showed only a intergranular fracture. An addition of only 0.05 wt.% of ZnO was also found to enhance the hardness and dielectric and ferroelectric properties of the PMNT ceramics.
Investigating the influence of PFC transection and nicotine on dynamics of AMPA and NMDA receptors of VTA dopaminergic neurons
Authors: Chen Ting , Zhang Die , Dragomir Andrei , Kobayashi Kunikazu , Akay Yasemin , Akay Metin 
Published: January 2012

AbstractBackgroundAll drugs of abuse, including nicotine, activate the mesocorticolimbic system that plays critical roles in nicotine reward and reinforcement development and triggers glutamatergic synaptic plasticity on the dopamine (DA) neurons in the ventral tegmental area (VTA). The addictive behavior and firing pattern of the VTA DA neurons are thought to be controlled by the glutamatergic synaptic input from prefrontal cortex (PFC). Interrupted functional input from PFC to VTA was shown to decrease the effects of the drug on the addiction process. Nicotine treatment could enhance the AMPA/NMDA ratio in VTA DA neurons, which is thought as a common addiction mechanism. In this study, we investigate whether or not the lack of glutamate transmission from PFC to VTA could make any change in the effects of nicotine.MethodsWe used the traditional AMPA/NMDA peak ratio, AMPA/NMDA area ratio, and KL (Kullback-Leibler) divergence analysis method for the present study.ResultsOur results using AMPA/NMDA peak ratio showed insignificant difference between PFC intact and transected and treated with saline. However, using AMPA/NMDA area ratio and KL divergence method, we observed a significant difference when PFC is interrupted with saline treatment. One possible reason for the significant effect that the PFC transection has on the synaptic responses (as indicated by the AMPA/NMDA area ratio and KL divergence) may be the loss of glutamatergic inputs. The glutamatergic input is one of the most important factors that contribute to the peak ratio level.ConclusionsOur results suggested that even within one hour after a single nicotine injection, the peak ratio of AMPA/NMDA on VTA DA neurons could be enhanced.
Evolution before genes
Authors: Vasas Vera , Fernando Chrisantha , Santos Mauro , Kauffman Stuart , Szathmáry Eörs 
Published: January 2012

AbstractBackgroundOur current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication.ResultsWe cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype).ConclusionsWe conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.ReviewersThis article was reviewed by William Martin and Eugene Koonin.
Effects of Gyejibongnyeong-hwan on dysmenorrhea caused by blood stagnation: study protocol for a randomized controlled trial
Authors: Park Jeong-Su , Park Sunju , Cheon Chun-Hoo , Go Ho-Yeon , Sun Seung-Ho , Shin Yong-Cheol , Jang Bo-Hyoung , Ko Seong-Gyu 
Published: January 2012

Abstract

Background
Gyejibongnyeong-hwan (GJBNH) is one of the most popular Korean medicine formulas for menstrual pain of dysmenorrhea. The concept of blood stagnation in Korean medicine is considered the main factor of causing abdominal pain, or cramps, during menstrual periods. To treat the symptoms, GJBNH is used to fluidify the stagnated blood and induce the blood flow to be smooth, reducing pain as the result. The purpose of this trial is to identify the efficacy of GJBNH in dysmenorrhea caused by blood stagnation.

Methods
This study is a multi-centre, randomised, double-blind, controlled trial with two parallel arms: the group taking GJBNH and the group taking placebo. 100 patients (women from age 18 to 35) will be enrolled to the trial. Through randomization 50 patients will be in experiment arm, and the other 50 patients will be in control arm. At the second visit (baseline), all participants who were already screened that they fulfil both the inclusion and the exclusion criteria will be randomised into two groups. Each group will take the intervention three times per day during two menstrual cycles. After the treatment for two cycles, each patient will be followed up during their 3rd, 4th and 5th menstrual cycles. From the screening (Visit 1) through the second follow-up (Visit 6) the entire process will take 25 weeks.

Discussion
This trial will provide evidence for the effectiveness of GJBNH in treating periodical pain due to dysmenorrhea that is caused by blood stagnation. The primary outcome between the two groups will be measured by changes in the Visual Analogue Score (VAS) of pain. The secondary outcome will be measured by the Blood Stagnation Scale, the Short-form McGill questionnaire and the COX menstrual symptom scale. Analysis of covariance (ANCOVA) and repeated measured ANOVA will be used to analyze the data analysis.

Trial registration
Current Controlled Trials: ISRCTN30426947