bluuebunny/crossref_metadata_2025_split huggingface dataset:
GC content around splice sites affects splicing through pre-mRNA secondary structures
Authors: Zhang Jing , Kuo CC Jay , Chen Liang 
Published: February 2011

Abstract

Background
Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens), mice (Mus musculus), fruit flies (Drosophila melanogaster), and nematodes (Caenorhabditis elegans) to further investigate this phenomenon.

Results
We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures.

Conclusion
All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.
T cells fail to develop in the human skin-cell explants system; an inconvenient truth
Authors: Meek Bob , Van Elssen Catharina HMJ , Huijskens Mirelle JAJ , van der Stegen Sjoukje JC , Tonnaer Siebe , Lumeij Stijn BJ , Vanderlocht Joris , Kirkland Mark A , Hesselink Reinout , Germeraad Wilfred TV , Bos Gerard MJ 
Published: February 2011

Abstract

Background
Haplo-identical hematopoietic stem cell (HSC) transplantation is very successful in eradicating haematological tumours, but the long post-transplant T-lymphopenic phase is responsible for high morbidity and mortality rates. Clark et al. have described a skin-explant system capable of producing host-tolerant donor-HSC derived T-cells. Because this T-cell production platform has the potential to replenish the T-cell levels following transplantation, we set out to validate the skin-explant system.

Results
Following the published procedures, while using the same commercial components, it was impossible to reproduce the skin-explant conditions required for HSC differentiation towards mature T-cells. The keratinocyte maturation procedure resulted in fragile cells with minimum expression of delta-like ligand (DLL). In most experiments the generated cells failed to adhere to carriers or were quickly outcompeted by fibroblasts. Consequently it was not possible to reproduce cell-culture conditions required for HSC differentiation into functional T-cells. Using cell-lines over-expressing DLL, we showed that the antibodies used by Clark et al. were unable to detect native DLL, but instead stained 7AAD+ cells. Therefore, it is unlikely that the observed T-lineage commitment from HSC is mediated by DLL expressed on keratinocytes. In addition, we did confirm expression of the Notch-ligand Jagged-1 by keratinocytes.

Conclusions
Currently, and unfortunately, it remains difficult to explain the development or growth of T-cells described by Clark et al., but for the fate of patients suffering from lymphopenia it is essential to both reproduce and understand how these co-cultures really "work". Fortunately, alternative procedures to speed-up T-cell reconstitution are being established and validated and may become available for patients in the near future.
The effect of experimental warming on leaf functional traits, leaf structure and leaf biochemistry in Arabidopsis thaliana
Authors: Jin Biao , Wang Li , Wang Jing , Jiang Ke-Zhen , Wang Yang , Jiang Xiao-Xue , Ni Cheng-Yang , Wang Yu-Long , Teng Nian-Jun 
Published: February 2011

Abstract

Background
The leaf is an important plant organ, and how it will respond to future global warming is a question that remains unanswered. The effects of experimental warming on leaf photosynthesis and respiration acclimation has been well studied so far, but relatively little information exists on the structural and biochemical responses to warming. However, such information is very important to better understand the plant responses to global warming. Therefore, we grew Arabidopsis thaliana at the three day/night temperatures of 23/18°C (ambient temperature), 25.5/20.5°C (elevated by 2.5°C) and 28/23°C (elevated by 5°C) to simulate the middle and the upper projected warming expected within the 21st century for this purpose.

Results
The 28/23°C treatment significantly reduced the life span, total biomass and total weight of seeds compared with the other two temperatures. Among the three temperature regimes, the concentrations of starch, chlorophyll, and proline were the lowest at 28/23°C, whereas the total weight of seeds, concentrations of chlorophyll and proline, stomatal density (SD), stomatal conductance (gs), net CO2 assimilation rate (A) and transpiration rate (E) were the highest at 25.5/20.5°C. Furthermore, the number of chloroplasts per cell and mitochondrial size were highest at 25.5/20.5°C and lowest at 28/23°C.

Conclusions
The conditions whereby the temperature was increased by 2.5°C were advantageous for Arabidopsis. However, a rise of 5°C produced negative effects, suggesting that lower levels of warming may benefit plants, especially those which belong to the same functional group as Arabidopsis, whereas higher levels of warming may produce negative affects. In addition, the increase in A under moderately warm conditions may be attributed to the increase in SD, chlorophyll content, and number of chloroplasts. Furthermore, starch accumulation in chloroplasts may be the main factor influencing chloroplast ultrastructure, and elevated temperature regulates plant respiration by probably affecting mitochondrial size. Finally, high SOD and CAT activities may enable plants grown at elevated temperatures to exhibit relatively high tolerance to temperature stress, thus alleviating the harmful effects of superoxide anion radicals and hydrogen peroxide.
Trends in self-reported prevalence and management of hypertension, hypercholesterolemia and diabetes in Swiss adults, 1997-2007
Authors: Estoppey Daniel , Paccaud Fred , Vollenweider Peter , Marques-Vidal Pedro 
Published: February 2011

Abstract

Background
Switzerland has a low mortality rate from cardiovascular diseases, but little is known regarding prevalence and management of cardiovascular risk factors (CV RFs: hypertension, hypercholesterolemia and diabetes) in the general population. In this study, we assessed 10-year trends in self-reported prevalence and management of cardiovascular risk factors in Switzerland.

Methods
data from three national health interview surveys conducted between 1997 and 2007 in representative samples of the Swiss adult population (49,261 subjects overall). Self-reported CV RFs prevalence, treatment and control levels were computed. The sample was weighted to match the sex - and age distribution, geographical location and nationality of the entire adult population of Switzerland.

Results
self-reported prevalence of hypertension, hypercholesterolemia and diabetes increased from 22.1%, 11.9% and 3.3% in 1997 to 24.1%, 17.4% and 4.8% in 2007, respectively. Prevalence of self-reported treatment among subjects with CV RFs also increased from 52.1%, 18.5% and 50.0% in 1997 to 60.4%, 38.8% and 53.3% in 2007 for hypertension, hypercholesterolemia and diabetes, respectively. Self-reported control levels increased from 56.4%, 52.9% and 50.0% in 1997 to 80.6%, 75.1% and 53.3% in 2007 for hypertension, hypercholesterolemia and diabetes, respectively. Finally, screening during the last 12 months increased from 84.5%, 86.5% and 87.4% in 1997 to 94.0%, 94.6% and 94.1% in 2007 for hypertension, hypercholesterolemia and diabetes, respectively.

Conclusion
in Switzerland, the prevalences of self-reported hypertension, hypercholesterolemia and diabetes have increased between 1997 and 2007. Management and screening have improved, but further improvements can still be achieved as over one third of subjects with reported CV RFs are not treated.
Toward nanofluids of ultra-high thermal conductivity
Authors: Wang Liqiu , Fan Jing 
Published: February 2011

AbstractThe assessment of proposed origins for thermal conductivity enhancement in nanofluids signifies the importance of particle morphology and coupled transport in determining nanofluid heat conduction and thermal conductivity. The success of developing nanofluids of superior conductivity depends thus very much on our understanding and manipulation of the morphology and the coupled transport. Nanofluids with conductivity of upper Hashin-Shtrikman (H-S) bound can be obtained by manipulating particles into an interconnected configuration that disperses the base fluid and thus significantly enhancing the particle-fluid interfacial energy transport. Nanofluids with conductivity higher than the upper H-S bound could also be developed by manipulating the coupled transport among various transport processes, and thus the nature of heat conduction in nanofluids. While the direct contributions of ordered liquid layer and particle Brownian motion to the nanofluid conductivity are negligible, their indirect effects can be significant via their influence on the particle morphology and/or the coupled transport.
Interplay between HIV Entry and Transportin-SR2 Dependency
Authors: Thys Wannes , De Houwer Stéphanie , Demeulemeester Jonas , Taltynov Oliver , Vancraenenbroeck Renée , Gérard Melanie , De Rijck Jan , Gijsbers Rik , Christ Frauke , Debyser Zeger 
Published: February 2011

Abstract

Background
Transportin-SR2 (TRN-SR2, TNPO3, transportin 3) was previously identified as an interaction partner of human immunodeficiency virus type 1 (HIV-1) integrase and functions as a nuclear import factor of HIV-1. A possible role of capsid in transportin-SR2-mediated nuclear import was recently suggested by the findings that a chimeric HIV virus, carrying the murine leukemia virus (MLV) capsid and matrix proteins, displayed a transportin-SR2 independent phenotype, and that the HIV-1 N74D capsid mutant proved insensitive to transportin-SR2 knockdown.

Results
Our present analysis of viral specificity reveals that TRN-SR2 is not used to the same extent by all lentiviruses. The DNA flap does not determine the TRN-SR2 requirement of HIV-1. We corroborate the TRN-SR2 independent phenotype of the chimeric HIV virus carrying the MLV capsid and matrix proteins. We reanalyzed the HIV-1 N74D capsid mutant in cells transiently or stably depleted of transportin-SR2 and confirm that the N74D capsid mutant is independent of TRN-SR2 when pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G). Remarkably, although somewhat less dependent on TRN-SR2 than wild type virus, the N74D capsid mutant carrying the wild type HIV-1 envelope required TRN-SR2 for efficient replication. By pseudotyping with envelopes that mediate pH-independent viral uptake including HIV-1, measles virus and amphotropic MLV envelopes, we demonstrate that HIV-1 N74D capsid mutant viruses retain partial dependency on TRN-SR2. However, this dependency on TRN-SR2 is lost when the HIV N74D capsid mutant is pseudotyped with envelopes mediating pH-dependent endocytosis, such as the VSV-G and Ebola virus envelopes.

Conclusion
Here we discover a link between the viral entry of HIV and its interaction with TRN-SR2. Our data confirm the importance of TRN-SR2 in HIV-1 replication and argue for careful interpretation of experiments performed with VSV-G pseudotyped viruses in studies on early steps of HIV replication including the role of capsid therein.
Vaccination with live attenuated simian immunodeficiency virus causes dynamic changes in intestinal CD4+CCR5+ T cells
Authors: Li Bo , Berry Neil , Ham Claire , Ferguson Deborah , Smith Deborah , Hall Joanna , Page Mark , Quartey-Papafio Ruby , Elsley William , Robinson Mark , Almond Neil , Stebbings Richard 
Published: February 2011

Abstract

Background
Vaccination with live attenuated SIV can protect against detectable infection with wild-type virus. We have investigated whether target cell depletion contributes to the protection observed. Following vaccination with live attenuated SIV the frequency of intestinal CD4+CCR5+ T cells, an early target of wild-type SIV infection and destruction, was determined at days 3, 7, 10, 21 and 125 post inoculation.

Results
In naive controls, modest frequencies of intestinal CD4+CCR5+ T cells were predominantly found within the LPL TTrM-1 and IEL TTrM-2 subsets. At day 3, LPL and IEL CD4+CCR5+ TEM cells were dramatically increased whilst less differentiated subsets were greatly reduced, consistent with activation-induced maturation. CCR5 expression remained high at day 7, although there was a shift in subset balance from CD4+CCR5+ TEM to less differentiated TTrM-2 cells. This increase in intestinal CD4+CCR5+ T cells preceded the peak of SIV RNA plasma loads measured at day 10. Greater than 65.9% depletion of intestinal CD4+CCR5+ T cells followed at day 10, but overall CD4+ T cell homeostasis was maintained by increased CD4+CCR5- T cells. At days 21 and 125, high numbers of intestinal CD4+CCR5- naive TN cells were detected concurrent with greatly increased CD4+CCR5+ LPL TTrM-2 and IEL TEM cells at day 125, yet SIV RNA plasma loads remained low.

Conclusions
This increase in intestinal CD4+CCR5+ T cells, following vaccination with live attenuated SIV, does not correlate with target cell depletion as a mechanism of protection. Instead, increased intestinal CD4+CCR5+ T cells may correlate with or contribute to the protection conferred by vaccination with live attenuated SIV.
Relative survival: a useful tool to assess generalisability in longitudinal studies of health in older persons
Authors: Hockey Richard , Tooth Leigh , Dobson Annette 
Published: February 2011

Abstract
Background
Generalisability of longitudinal studies is threatened by issues such as choice of sampling frame, representativeness of the initial sample, and attrition. To determine representativeness, cohorts are often compared with the population of interest at baseline on demographic and health characteristics. This study illustrates the use of relative survival as a tool for assessing generalisability of results from a cohort of older people among whom death is a potential threat to generalisability.

Methods
The authors used data from the 1921-26 cohort (n = 12,416, aged 70-75 in 1996) of the Australian Longitudinal Study on Women's Health (ALSWH). Vital status was determined by linkage to the National Death Index, and expected deaths were derived using Australian life tables. Relative survival was estimated using observed survival in the cohort divided by expected survival among women of the same age and State or Territory.

Results
Overall, the ALSWH women showed relative survival 9.5% above the general population. Within States and Territories, the relative survival advantage varied from 6% to 23%. The interval-specific relative survival remained relatively constant over the 12 years (1996-2008) under review, indicating that the survival advantage of the cohort has not diminished over time.

Conclusion
This study demonstrates that relative survival can be a useful measure of generalisability in a longitudinal study of the health of the general population, particularly when participants are older.
Spatial and temporal EEG dynamics of dual-task driving performance
Authors: Lin Chin-Teng , Chen Shi-An , Chiu Tien-Ting , Lin Hong-Zhang , Ko Li-Wei 
Published: February 2011

Abstract

Background
Driver distraction is a significant cause of traffic accidents. The aim of this study is to investigate Electroencephalography (EEG) dynamics in relation to distraction during driving. To study human cognition under a specific driving task, simulated real driving using virtual reality (VR)-based simulation and designed dual-task events are built, which include unexpected car deviations and mathematics questions.

Methods
We designed five cases with different stimulus onset asynchrony (SOA) to investigate the distraction effects between the deviations and equations. The EEG channel signals are first converted into separated brain sources by independent component analysis (ICA). Then, event-related spectral perturbation (ERSP) changes of the EEG power spectrum are used to evaluate brain dynamics in time-frequency domains.

Results
Power increases in the theta and beta bands are observed in relation with distraction effects in the frontal cortex. In the motor area, alpha and beta power suppressions are also observed. All of the above results are consistently observed across 15 subjects. Additionally, further analysis demonstrates that response time and multiple cortical EEG power both changed significantly with different SOA.

Conclusions
This study suggests that theta power increases in the frontal area is related to driver distraction and represents the strength of distraction in real-life situations.
The effects of attention capacity on dynamic balance control following concussion
Authors: Catena Robert D , van Donkelaar Paul , Chou Li-Shan 
Published: February 2011

Abstract
The purpose of this study was to examine how individuals modulate attention in a gait/cognition dual task during a 4-week period following a concussion. Ten individuals suffering from a grade 2 concussion and 10 matched controls performed a single task of level walking, a seated auditory Stroop task and a simultaneous auditory Stroop and walking task. Reaction time and accuracy were measured from the Stroop task. Dynamic balance control during gait was measured by the interaction (displacement and velocity) between the center of mass (CoM) and center of pressure (CoP) in the coronal and sagittal planes. Concussed individuals shifted from conservative control of balance (shorter separation between CoM and CoP) immediately after injury to normal balance control over 28 days post-injury. Immediately after injury, correlations analyses using each subject on each testing day as a data point showed that there was a spectrum of deficient performance among concussed individuals on the first testing day. Within a testing session, deficiencies in reaction time of processing involved in the Stroop task were commonly seen with reduce dynamic balance control. However, the prioritization was not always towards the same task between trials. There were no correlations in the control group. Information provided in this study would enhance our understanding of the interaction between attention and gait following concussion.
Licorice consumption as a cause of posterior reversible encephalopathy syndrome: a case report
Authors: van Beers Eduard J , Stam Jan , van den Bergh Walter M 
Published: February 2011

Abstract
Introduction
A 49-year-old woman was admitted to our hospital because of thunderclap headache and blurred vision. At the time of presentation, her blood pressure was 219/100 mmHg, her arterial pH was 7.64 and her potassium level was 2.7 mM/l.

Methods
The combination of sequential computed tomography (CT) and the triad of hypertension, hypokalemia and metabolic alkalosis in this patient suggested the diagnosis. Supplementary anamnesis and long-term follow-up confirmed it.

Results
Brain computed tomography imaging showed minor bleeding in the left Sylvian fissure and bilateral occipital edema, suggestive of posterior reversible encephalopathy syndrome (PRES). Repeated brain CT after 10 days showed a complete resolution of radiological signs. The patient informed us that she had quit smoking 2 weeks ago and had started consuming large amounts of licorice instead of smoking. After she abandoned licorice consumption, her blood pressure normalized. Her latest blood pressure reading was 106/60 mmHg without the use of any antihypertensive drugs.

Conclusions
To the best of our knowledge, this is the first case report describing licorice consumption as a cause of PRES. Glycyrrhizic acid, a component of licorice, inhibits 11β-hydroxysteroid dehydrogenase and subsequently causes mineralocorticoid excess. Mineralocorticoid excess in turn causes high blood pressure and ultimately gives rise to malignant hypertension. Physicians should remember that licorice use is a very easy-to-treat cause of hypertension, hypertensive encephalopathy and PRES.
CD154-CD40 interactions in the control of murine B cell hematopoiesis
Authors: Carlring Jennifer , Altaher Hala M , Clark Susan , Chen Xi , Latimer Sarah L , Jenner Tracey , Buckle Anne-Marie , Heath Andrew W 
Published: February 2011

ABSTRACTInteractions between CD40 and CD154 play a very important role in control of immune responses, including the delivery of T cell help to B cells and other APCs. Thus far, there has been no role postulated for CD40-CD154 interactions in hematopoiesis. We show here that CD40 is expressed on murine pro-B cells and that its ligation enhances pro-B cell proliferation in vitro and in vivo. In addition, CD154 mRNA is present in the BM. Moreover, we show that a deficiency in CD154 expression has effects on B cell hematopoiesis. Aged, CD154-deficient mice have significantly lower levels of B hematopoietic subsets downstream of pro-B cells in the BM. In addition, B lineage cells reconstitute more slowly following BMT into CD154-deficient recipients. We hypothesize that CD154 is expressed by radio-resistant cells in the BM and plays a role in fine-tuning B cell hematopoiesis.
Simvastatin antagonizes CD40L secretion, CXC chemokine formation, and pulmonary infiltration of neutrophils in abdominal sepsis
Authors: Zhang Su , Rahman Milladur , Zhang Songen , Qi Zhongquan , Thorlacius Henrik 
Published: February 2011

ABSTRACTStatins have been reported to exert anti-inflammatory actions and protect against septic organ dysfunction. Herein, we hypothesized that simvastatin may attenuate neutrophil activation and lung damage in abdominal sepsis. Male C57BL/6 mice were pretreated with simvastatin (0.5 or 10 mg/kg) before CLP. In separate groups, mice received an anti-CD40L antibody or a CXCR2 antagonist (SB225002) prior to CLP. BALF and lung tissue were harvested for analysis of neutrophil infiltration, as well as edema and CXC chemokine formation. Blood was collected for analysis of Mac-1 and CD40L expression on neutrophils and platelets, as well as soluble CD40L in plasma. Simvastatin decreased CLP-induced neutrophil infiltration and edema formation in the lung. Moreover, Mac-1 expression increased on septic neutrophils, which was significantly attenuated by simvastatin. Inhibition of CD40L reduced CLP-induced up-regulation of Mac-1 on neutrophils. Simvastatin prevented CD40L shedding from the surface of platelets and reduced circulating levels of CD40L in septic mice. CXC chemokine-induced migration of neutrophils in vitro was decreased greatly by simvastatin. Moreover, simvastatin abolished CLP-evoked formation of CXC chemokines in the lung, and a CXCR2 antagonist attenuated pulmonary accumulation of neutrophils. Our data suggest that the inhibitory effect of simvastatin on pulmonary accumulation of neutrophils may be related to a reduction of CD40L secretion into the circulation, as well as a decrease in CXC chemokine formation in the lung. Thus, these protective mechanisms help to explain the beneficial actions exerted by statins, such as simvastatin, in sepsis.