bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Highly Configurable Vortex Initialization Method for Tropical Cyclones
Authors: Rappin Eric D. , Nolan David S. , Majumdar Sharanya J. 
Published: May 2013

Abstract
A highly configurable vortex initialization methodology has been constructed in order to permit manipulation of the initial vortex structure in numerical models of tropical cyclones. By using distinct specifications of the flow in the boundary layer and free atmosphere, an array of parameters is available to modify the structure. A nonlinear similarity model that solves the steady-state, height-dependent equations for a neutrally stratified, axisymmetric vortex is solved for the boundary layer flow. Above the boundary layer, a steady-state, moist-neutral, hydrostatic and gradient wind balanced model is used to generate the angular momentum distribution in the free atmosphere. In addition, an unbalanced mass-conserving secondary circulation is generated through the assumption of conservation of mass and angular momentum above the boundary layer. Numerical simulations are conducted using a full-physics mesoscale model to explore the sensitivity of the vortex evolution to different prescriptions of the initial vortex. Dynamical adjustment is found to be dominant in the early evolution of the simulations, thereby masking any sensitivity to initial changes in the secondary circulation and boundary layer structure. The adjustment time can be significantly reduced by arbitrarily enhancing the moisture in the eyewall region.
Modification and characterization of bentonite with quaternary ammonium and phosphonium salts and its use in polypropylene nanocomposites
Authors: Seyidoglu Tijen , Yilmazer Ulku 
Published: May 2013

Montmorillonite-rich local bentonite was modified with four different quaternary alkyl salts: hexadecyltrimethylammonium bromide ((HMA)(Br)), tetra(kis)decylammonium bromide ((TKA)(Br)), tetrabutylammonium tetrafluoroborate ((TBA)(BF4)), and tetrabutylphosphonium tetrafluoroborate ((TBP)(BF4)) to produce organoclays. The organoclays produced were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis (TGA), and x-ray diffraction (XRD). The XRD results indicate that the d-spacing of the organoclays increased as a consequence of the exchange of Na+ ions in the clay galleries with the cation of the surfactants with long alkyl tails. The d-spacing of the bentonite increased from 1.2 nm to 1.78 nm, 2.56 nm, 1.48 nm, and 1.64 nm after modification with HMA, TKA, TBA, and TBP cations, respectively. TGA analysis of the organoclays showed that the decomposition temperatures of the organoclays were higher than the melt processing temperature of polypropylene (PP), permitting the use of these organoclays in melt processing of PP. Ternary composites of PP/PP-grafted maleic anhydride/organoclays were prepared using a twin screw extruder followed by injection molding for characterization. Transmission electron microscopy analysis of the composites showed intercalated structures as well as microcomposite formations. Mechanical properties of pure PP were improved through ternary composite formation.
Notch1 regulates angio-supportive bone marrow–derived cells in mice: relevance to chemoresistance
Authors: Roodhart Jeanine M. L. , He Huanhuan , Daenen Laura G. M. , Monvoisin Arnaud , Barber Chad L. , van Amersfoort Miranda , Hofmann Jennifer J. , Radtke Freddy , Lane Timothy F. , Voest Emile E. , Iruela-Arispe M. Luisa 
Published: May 2013

Key PointsExposure to chemotherapy promotes the exit of specific subpopulations of BMDCs with angio-supportive activity. Notch in BMDCs is required for the exit of these cells from the bone marrow and for chemotherapy-enhanced angiogenesis in tumors.
Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns
Authors: Savage Abigail L , Bubb Vivien J , Breen Gerome , Quinn John P 
Published: May 2013

AbstractBackgroundRetrotransposons are a major component of the human genome constituting as much as 45%. The hominid specific SINE-VNTR-Alus are the youngest of these elements constituting 0.13% of the genome; they are therefore a practical and amenable group for analysis of both their global integration, polymorphic variation and their potential contribution to modulation of genome regulation.ResultsConsistent with insertion into active chromatin we have determined that SVAs are more prevalent in genic regions compared to gene deserts. The consequence of which, is that their integration has greater potential to have affects on gene regulation. The sequences of SVAs show potential for the formation of secondary structure including G-quadruplex DNA. We have shown that the human specific SVA subtypes (E-F1) show the greatest potential for forming G-quadruplexes within the central tandem repeat component in addition to the 5’ ‘CCCTCT’ hexamer. We undertook a detailed analysis of thePARK7SVA D, located in the promoter of thePARK7gene (also termedDJ-1), in a HapMap cohort where we identified 2 variable number tandem repeat domains and 1 tandem repeat within this SVA with the 5’ CCCTCT element being one of the variable regions. Functionally we were able to demonstrate that this SVA contains multiple regulatory elements that support reporter gene expressionin vitroand further show these elements exhibit orientation dependency.ConclusionsOur data supports the hypothesis that SVAs integrate preferentially in to open chromatin where they could modify the existing transcriptional regulatory domains or alter expression patterns by a variety of mechanisms.
Predictors of suicidal behaviour in 36,304 individuals sickness absent due to stress-related mental disorders - a Swedish register linkage cohort study
Authors: Ishtiak-Ahmed Kazi , Perski Aleksander , Mittendorfer-Rutz Ellenor 
Published: May 2013

Abstract

Background
Stress-related mental disorders (SRMD), which correspond to the diagnostic code F43 in the International Classification of Diseases, version 10, rank among the leading causes of sickness absence in several European countries. Despite the size of this health problem, research on risk factors for severe medical outcomes, like suicidal behavior, is lacking to date. The aim of this study was to investigate predictors of suicide attempt and suicide among sickness absentees with SRMD.

Methods
A cohort of 36,304 non-retired individuals, aged 16–64 years on 31.12.2004, with at least one sickness absence spell due to SRMD, initiated in 2005, was followed up with regard to suicide attempt (2006–2009) and suicide (2006–2008). Univariate and multivariate hazard ratios (HR) with 95% confidence intervals (CI) were estimated for a number of predictors.

Results
During the follow-up period, 266 individuals attempted suicide and 34 committed suicide. In the multivariate analyses, the following factors increased the risk of suicide attempt: =< 25 years of age, low educational level, lone parenthood, > 1 sickness absence spell, long duration of the first spell of sickness absence due to SRMD (> 180 days), > 4 and > 8 days of inpatient care due to somatic or mental diagnoses (2000–2005), and > 4 and > 1 outpatient visits due to somatic or mental diagnoses (2001–2005), respectively. Hazard ratios ranged from 1.4 to 4.2. Health care due to mental diagnoses and > 1 spell of sickness absence regardless of diagnosis were predictive of suicide.

Conclusions
Several predictors related to socio-demographics, sickness absence and health-care consumption were identified as risk factors for suicidal behavior. Consideration of these risk factors is of both clinical and public health importance.
In situ magnetic separation of antibody fragments from Escherichia coli in complex media
Authors: Cerff Martin , Scholz Alexander , Franzreb Matthias , Batalha Iris L , Roque Ana Cecilia A , Posten Clemens 
Published: May 2013

Abstract

Background
In situ magnetic separation (ISMS) has emerged as a powerful tool to overcome process constraints such as product degradation or inhibition of target production. In the present work, an integrated ISMS process was established for the production of his-tagged single chain fragment variable (scFv) D1.3 antibodies (“D1.3”) produced by E. coli in complex media. This study investigates the impact of ISMS on the overall product yield as well as its biocompatibility with the bioprocess when metal-chelate and triazine-functionalized magnetic beads were used.

Results
Both particle systems are well suited for separation of D1.3 during cultivation. While the triazine beads did not negatively impact the bioprocess, the application of metal-chelate particles caused leakage of divalent copper ions in the medium. After the ISMS step, elevated copper concentrations above 120 mg/L in the medium negatively influenced D1.3 production. Due to the stable nature of the model protein scFv D1.3 in the biosuspension, the application of ISMS could not increase the overall D1.3 yield as was shown by simulation and experiments.

Conclusions
We could demonstrate that triazine-functionalized beads are a suitable low-cost alternative to selectively adsorb D1.3 fragments, and measured maximum loads of 0.08 g D1.3 per g of beads. Although copper-loaded metal-chelate beads did adsorb his-tagged D1.3 well during cultivation, this particle system must be optimized by minimizing metal leakage from the beads in order to avoid negative inhibitory effects on growth of the microorganisms and target production. Hereby, other types of metal chelate complexes should be tested to demonstrate biocompatibility. Such optimized particle systems can be regarded as ISMS platform technology, especially for the production of antibodies and their fragments with low stability in the medium. The proposed model can be applied to design future ISMS experiments in order to maximize the overall product yield while the amount of particles being used is minimized as well as the number of required ISMS steps.
Water extract of Spatholobus suberectus inhibits osteoclast differentiation and bone resorption
Authors: Ha Hyunil , Shim Ki-Shuk , An Hyosun , Kim Taesoo , Ma Jin Yeul 
Published: May 2013

Abstract

Background
Osteoclasts are primarily responsible for bone resorption. In many pathological bone diseases including osteoporosis and rheumatoid arthritis, osteoclasts are excessively activated. Thus, controlling of osteoclasts would be an effective therapeutic strategy for the treatment of excessive bone loss. The stem of Spatholobus suberectus has been widely used in traditional medicine to treat blood stasis syndrome and arthritis in Asia. In the present study, we investigated the effects and action mechanism of water extract of the stem of Spatholobus suberectus (WESS) on osteoclast differentiation and function.

Methods
The effect of WESS on osteoclast differentiation was evaluated by counting tartrate resistant acid phosphatase-positive multinucleated cells in bone marrow-derived macrophages system and murine bone marrow cell-osteoblast coculture system. Bone resorption activity of mature osteoclast was examined on a calcium phosphate-coated plate. Actin ring structure of osteoclasts was detected fluorescently by staining for F-actin. Activation of signaling pathways and induction of transcription factors required for osteoclastogenesis were investigated by real-time PCR and Western blotting.

Results
WESS effectively inhibited osteoclast differentiation from its precursors. The inhibitory effect of WESS on osteoclast differentiation was due to the suppression of osteoclastogenic transcription factors, c-Fos and nuclear factor of activated T cells cytoplasmic 1 expression, via preventing receptor activator of nuclear factor-κB ligand-induced early signaling pathways and decreasing c-Fos protein level in osteoclast precursors. Furthermore, WESS suppressed bone resorption activity of osteoclasts by disrupting actin ring structure.

Conclusions
This study demonstrated that WESS inhibits osteoclast differentiation and function. These results suggest that WESS has a potential for treating pathological bone diseases caused by excessive bone resorption.
Application of propensity scores to estimate the association between government subsidy and injection use in primary health care institutions in China
Authors: Tang Yuqing , Zhang Xiaopeng , Yang Chunyan , Yang Lianping , Wang Hongtao , Zhang Xinping 
Published: May 2013

Abstract

Background
The problem posed by therapeutic injection is a clinical practice issue that influences health care quality and patient safety. Although sufficient government subsidy was one of the 12 key interventions to promote rational drug use initiated by WHO (World Health Organization), limited information is available about the association between government subsidy and injection use in primary health care institutions. In 2009, National Essential Medicines System (NEMS) was implemented in China. The subsidy policy plays an important role in maintaining primary health care institutions. This study explores the impact of government subsidies on the injection use in primary health care institutions in China.

Methods
126 primary health institutions were included in this study. Institutions were divided into two groups (intervention and control groups) according to the median GS (General subsidy per personnel). Propensity score matching (PSM) was used to minimize the observed covariate differences in the characteristics of the primary institutions between the two groups. Kappa score was calculated to determine the consistency between the groups. Paired chi-square test and Relative Risk (RR) were calculated to compare the differences in injection use between the groups.

Results
Among all the investigated prescriptions, the overall percent of people who received an injection prescribed was 36.96% (n = 12600). PSM showed no significant covariate difference among the 34 groups obtained through this analysis. Kappa score (k = −0.082, p = 0.558) indicated an inconsistency between groups and paired chi-square test revealed a significant difference (p < 0.05) in injection use between the two groups. Relative Risk = 0.679 (95%CI [0.485, 0.950]) indicate that high General subsidy per personnel is a protective factor for primary health care institutions to prescribe injections properly. The intervention group obtained a higher possibility of using injection properly.

Conclusions
The overall effect of government subsidy on the use of injection was positively significant. However, the mechanism by which government subsidy influence injection administration remains unclear, and thus requires further study.
Polymorphism of the parasite lactate dehydrogenase gene from Plasmodium vivax Korean isolates
Authors: Shin Hyun-Il , Kim Jung-Yeon , Lee Won-Ja , Sohn Youngjoo , Lee Sang-Wook , Kang Yoon-Joong , Lee Hyeong-Woo 
Published: May 2013

Abstract

Background
Assaying for the parasitic lactate dehydrogenase (pLDH) is widely used as a rapid diagnostic test (RDT), but the efficacy of its serological effectiveness in diagnosis, that is antibody detection ability, is not known. The genetic variation of Korean isolates was analysed, and recombinant protein pLDH was evaluated as a serodiagnostic antigen for the detection of Plasmodium vivax malaria.

Methods
Genomic DNA was purified, and the pLDH gene of P. vivax was amplified from blood samples from 20 patients. The samples came from five epidemic areas: Bucheon-si, Gimpo-si, and Paju-si of Gyeonggi Province, Gangwha-gun of Incheon metropolitan city, and Cheorwon-gun of Gangwon Province, South Korea, from 2010 to 2011. The antigenicity of the recombinant protein pLDH was tested by western blot and enzyme-linked immunosorbent assay (ELISA).

Results
Sequence analysis of 20 Korean isolates of P. vivax showed that the open reading frame (ORF) of 951 nucleotides encoded a deduced protein of 316 amino acids (aa). This ORF showed 100% identity with the P. vivax Belem strain (DQ060151) and P. vivax Hainan strain (FJ527750), 89.6% homology with Plasmodium falciparum FCC1_HN (DQ825436), 90.2% homology with Plasmodium berghei (AY437808), 96.8% homology with Plasmodium knowlesi (JF958130), and 90.2% homology with Plasmodium reichenowi (AB122147). A single-nucleotide polymorphism (SNP) at nucleotide 456 (T to C) was also observed in the isolate from Bucheon, but it did not change in the amino acid sequence. The expressed recombinant protein had a molecular weight of approximately 32 kDa, as analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. Of the 40 P. vivax patients, 34 (85.0%) were positive by ELISA.

Conclusions
The pLDH genes of 19 isolates of P. vivax were identical, except one for SNP at nucleotide 456. This observation indicates that this gene is relatively stable. Based on these results, the relationship between antibody production against pLDH and the pattern of disease onset should be investigated further before using pLDH for serodiagnosis.
Activation of Akt pathway by transcription-independent mechanisms of retinoic acid promotes survival and invasion in lung cancer cells
Authors: García-Regalado Alejandro , Vargas Miguel , García-Carrancá Alejandro , Aréchaga-Ocampo Elena , González-De la Rosa Claudia Haydée 
Published: May 2013

Abstract

Background
All-trans retinoic acid (ATRA) is currently being used in clinical trials for cancer treatment. The use of ATRA is limited because some cancers, such as lung cancer, show resistance to treatment. However, little is known about the molecular mechanisms that regulate resistance to ATRA treatment. Akt is a kinase that plays a key role in cell survival and cell invasion. Akt is often activated in lung cancer, suggesting its participation in resistance to chemotherapy. In this study, we explored the hypothesis that activation of the Akt pathway promotes resistance to ATRA treatment at the inhibition of cell survival and invasion in lung cancer. We aimed to provide guidelines for the proper use of ATRA in clinical trials and to elucidate basic biological mechanisms of resistance.

Results
We performed experiments using the A549 human lung adenocarcinoma cell line. We found that ATRA treatment promotes PI3k-Akt pathway activation through transcription-independent mechanisms. Interestingly, ATRA treatment induces the translocation of RARα to the plasma membrane, where it colocalizes with Akt. Immunoprecipitation assays showed that ATRA promotes Akt activation mediated by RARα-Akt interaction. Activation of the PI3k-Akt pathway by ATRA promotes invasion through Rac-GTPase, whereas pretreatment with 15e (PI3k inhibitor) or over-expression of the inactive form of Akt blocks ATRA-induced invasion. We also found that treatment with ATRA induces cell survival, which is inhibited by 15e or over-expression of an inactive form of Akt, through a subsequent increase in the levels of the active form of caspase-3. Finally, we showed that over-expression of the active form of Akt significantly decreases expression levels of the tumor suppressors RARβ2 and p53. In contrast, over-expression of the inactive form of Akt restores RARβ2 expression in cells treated with ATRA, indicating that activation of the PI3k-Akt pathway inhibits the expression of ATRA target genes.

Conclusion
Our results demonstrate that rapid activation of Akt blocks transcription-dependent mechanism of ATRA, promotes invasion and cell survival and confers resistance to retinoic acid treatment in lung cancer cells. These findings provide an incentive for the design and clinical testing of treatment regimens that combine ATRA and PI3k inhibitors for lung cancer treatment.
Depletion of polycistronic transcripts using short interfering RNAs: cDNA synthesis method affects levels of non-targeted genes determined by quantitative PCR
Authors: Hanning Jennifer E , Groves Ian J , Pett Mark R , Coleman Nicholas 
Published: May 2013

Abstract

Background
Short interfering RNAs (siRNAs) are often used to deplete viral polycistronic transcripts, such as those encoded by human papillomavirus (HPV). There are conflicting data in the literature concerning how siRNAs targeting one HPV gene can affect levels of other genes in the polycistronic transcripts. We hypothesised that the conflict might be partly explained by the method of cDNA synthesis used prior to transcript quantification.

Findings
We treated HPV16-positive cervical keratinocytes with siRNAs targeting the HPV16 E7 gene and used quantitative PCR to compare transcript levels of E7 with those of E6 and E2, viral genes located upstream and downstream of the target site respectively. We compared our findings from cDNA generated using oligo-dT primers alone with those from cDNA generated using a combination of random hexamer and oligo-dT primers. Our data show that when polycistronic transcripts are targeted by siRNAs, there is a period when untranslatable cleaved mRNA upstream of the siRNA binding site remains detectable by PCR, if cDNA is generated using random hexamer primers. Such false indications of mRNA abundance are avoided using oligo-dT primers. The period corresponds to the time taken for siRNA activity and degradation of the cleaved transcripts. Genes downstream of the siRNA binding site are detectable during this interval, regardless of how the cDNA is generated.

Conclusions
These data emphasise the importance of the cDNA synthesis method used when measuring transcript abundance following siRNA depletion of polycistronic transcripts. They provide a partial explanation for erroneous reports suggesting that siRNAs targeting HPV E7 can have gene-specific effects.
Chlamydia felis exposure in companion dogs and cats in Lanzhou, China: a public health concern
Authors: Wu Song-Ming , Huang Si-Yang , Xu Min-Jun , Zhou Dong-Hui , Song Hui-Qun , Zhu Xing-Quan 
Published: May 2013

Abstract

Background
Chlamydiaceae is a family of obligate intracellular pathogens with a worldwide distribution in many animal species, including humans. No information exists on the prevalence of Chlamydia felis infections in cats and dogs in Lanzhou, the geographical center of China. The aim of this study was to carry out a census of cats and dogs in Lanzhou and document the seroprevalence of C. felis exposure in these companion animals.

Results
In this study, blood samples were collected from 485 animals (221 cats and 264 pet dogs) in Lanzhou between November 2010 and July 2011 to identify antibodies against C. felis. Thirteen of 221 (5.9%) cats and 32 of 264 (12.1%) pet dogs were positive for C. felis infection using indirect hemagglutination at a cutoff of 1:16. The seroprevalence in household and stray cats was 3.9% and 14.3%, respectively, and the difference was statistically significant (P < 0.05). Among different age groups, the seroprevalence in cats varied from 1.9 to 7.9%, and that in dogs ranged from 9.6 to 20.4%; however, the differences were not statistically significant (P > 0.05).

Conclusions
This is the first report of the seroprevalence of C. felis exposure in cats and dogs in Lanzhou, northwestern China. Our results indicate that the presence of C. felis exposure in cats and dogs may pose a potential threat to human health.