bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of differentially expressed genes in the Ras1CA-overexpressed and wildtype posterior silk glands
Authors: Ma Li , Ma Qian , Li Xuan , Cheng Leilei , Li Kai , Li Sheng 
Published: March 2014

Abstract

Background
Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1
CA oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecular mechanism remains to be fully elucidated. To achieve this goal, Illumina sequencing was used in the present study to compare the transcriptomes of the Ras1
CA-overexpressed and wildtype PSGs.

Results
The transcriptomic sequencing results in 56 million reads following filtering steps. Most of the reads (~70%) are successfully mapped to the Bombyx genome. The mapped reads are situated within at least 9,133 predicted genes, covering 62.46% genes of the Bombyx genome. GO annotation shows that 2512 of the 2,636 differentially expressed genes (DEGs) are mostly distributed in metabolic process, cell and cell part, and binding, and KEGG annotation shows that 1,941 DEGs are mapped into 277 pathways. Importantly, Ras1
CA overexpression in the PSG upregulated many DEGs distributed in “pathways in cancer”, “insulin signaling pathway”, and “MAPK signaling pathway” as well as “purine metabolism” and “pyrimidine metabolism”. Transcriptional regulation of these DEGs was verified by quantitative real-time PCR. Moreover, injection of small-molecule chemical inhibitors of the Ras1 downstream effectors into the Ras1
CA-overexpressed silkworms revealed that both Raf-MAPK and PI3K-TORC1 pathways are required for the Ras1-induced DEG expression.

Conclusion
The transcriptomic analysis illustrates that, apart from phosphorylational regulation, Ras1 activates its downstream Raf-MAPK and PI3K-TORC1 pathways at the transcriptional level. Meanwhile, Ras1 increases DNA content and induces endoreplication, at least in part, by upregulating genes in “nucleotide metabolism” and “cell cycle”. This study provides further insights into the molecular mechanism of how Ras1

CA
overexpression in the PSG improves silk yield.
Effect of melilotus extract on lung injury by upregulating the expression of cannabinoid CB2 receptors in septic rats
Authors: Liu Ming-wei , Su Mei-xian , Wang Yun-hui , Wei Wei , Qin Lan-fang , Liu Xu , Tian Mao-li , Qian Chuan-yun 
Published: March 2014

Abstract

Background

M. Suaveolens Ledeb has long been used in China to treat inflammatory infectious diseases. Melilotus is extracted from Melilotus Suaveolens Ledeb and its therapeutic potential is associated with its anti-inflammatory activity. However, the precise mechanisms underlying its effects are unknown. This study was conducted to evaluate the protective effects of melilotus extract in a rat cecal ligation and puncture (CLP)-induced animal model of acute lung injury (ALI).

Methods
A sepsis model was induced by CLP-like lung inflammation. Two hours prior to CLP administration, the treatment group was administered melilotus extract via oral injection. RT-PCR and Western blotting were used to test the expression of cannabinoid receptor (CB)2, NF-κβ and IκB from single peripheral blood mononuclear cells and lung tissues respectively. Enzyme linked immune sorbent assay was used to detect serum levels of tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-10, and IL-12. The numbers of neutrophils, lymphocytes, macrophages and total cells in the bronchoalveolar lavage (BAL) fluid were counted. For histologic analysis, hematoxylin and eosin (H&E) stains were evaluated.

Results
After inducing ALI by CLP for 24 hours, melilotus extract up-regulated peripheral blood mononuclear cell CB2 expression, blocked the activity of NF-κβ65, and the number of neutrophils, lymphocytes and total cells were significantly lower in the melilotus extract group than the control group. In addition, TNF-α and IL-6 levels were significantly decreased in the melilotus extract group. Histological results demonstrated the attenuation effect of melilotus extract on CLP-induced lung inflammation. CB2 was negatively correlated to NF-κβ mRNA and proteins, respectively (r = -0.377, P < 0.05; r = -0.441, P < 0.05).

Conclusion
The results of this study indicated melilotus extract significantly reduced CLP-induced lung inflammation by up-regulating CB2 expression. The remarkable protective effects of melilotus extract suggest its therapeutic potential in CLP induced-acute lung injury treatment.
Computer game-based upper extremity training in the home environment in stroke persons: a single subject design
Authors: Slijper Angelique , Svensson Karin E , Backlund Per , Engström Henrik , Sunnerhagen Katharina Stibrant 
Published: March 2014

AbstractBackgroundThe objective of the present study was to assess whether computer game-based training in the home setting in the late phase after stroke could improve upper extremity motor function.MethodsTwelve subjects with prior stroke were recruited; 11 completed the study.DesignThe study had a single subject design; there was a baseline test (A1), a during intervention test (B) once a week, a post-test (A2) measured directly after the treatment phase, plus a follow-up (C) 16–18 weeks after the treatment phase. Information on motor function (Fugl-Meyer), grip force (GrippitR) and arm function in activity (ARAT, ABILHAND) was gathered at A1, A2 and C. During B, only Fugl-Meyer and ARAT were measured. The intervention comprised five weeks of game-based computer training in the home environment. All games were designed to be controlled by either the affected arm alone or by both arms. Conventional formulae were used to calculate the mean, median and standard deviations. Wilcoxon’s signed rank test was used for tests of dependent samples. Continuous data were analyzed by methods for repeated measures and ordinal data were analyzed by methods for ordered multinomial data using cumulative logistic models. A p-value of < 0.05 was considered statistically significant.ResultsSix females and five males, participated in the study with an average age of 58 years (range 26–66). FMA-UE A-D (motor function), ARAT, the maximal grip force and the mean grip force on the affected side show significant improvements at post-test and follow-up compared to baseline. No significant correlation was found between the amount of game time and changes in the outcomes investigated in this study.ConclusionThe results indicate that computer game-based training could be a promising approach to improve upper extremity function in the late phase after stroke, since in this study, changes were achieved in motor function and activity capacity.
Intensity-Duration-Frequency (IDF) rainfall curves, for data series and climate projection in African cities
Authors: De Paola Francesco , Giugni Maurizio , Topa Maria Elena , Bucchignani Edoardo 
Published: March 2014

AbstractChanges in the hydrologic cycle due to increase in greenhouse gases cause variations in intensity, duration, and frequency of precipitation events. Quantifying the potential effects of climate change and adapting to them is one way to reduce urban vulnerability. Since rainfall characteristics are often used to design water structures, reviewing and updating rainfall characteristics (i.e., Intensity–Duration–Frequency (IDF) curves) for future climate scenarios is necessary (Reg Environ Change 13(1 Supplement):25-33, 2013).The present study regards the evaluation of the IDF curves for three case studies: Addis Ababa (Ethiopia), Dar Es Salaam (Tanzania) and Douala (Cameroon). Starting from daily rainfall observed data, to define the IDF curves and the extreme values in a smaller time window (10′, 30′, 1 h, 3 h, 6 h, 12 h), disaggregation techniques of the collected data have been used, in order to generate a synthetic sequence of rainfall, with statistical properties similar to the recorded data. Then, the rainfall pattern of the three test cities was analyzed and IDF curves were evaluated.In order to estimate the contingent influence of climate change on the IDF curves, the described procedure was applied to the climate (rainfall) simulations over the time period 2010–2050, provided by CMCC (Centro Euro-Mediterraneo sui Cambiamenti Climatici). The evaluation of the IDF curves allowed to frame the rainfall evolution of the three case studies, considering initially only historical data, then taking into account the climate projections, in order to verify the changes in rainfall patterns. The same set of data and projections was also used for evaluating the Probable Maximum Precipitation (PMP).
Angiotensin receptor type 1 and endothelin receptor type A on immune cells mediate migration and the expression of IL-8 and CCL18 when stimulated by autoantibodies from systemic sclerosis patients
Authors: Günther Jeannine , Kill Angela , Becker Mike Oliver , Heidecke Harald , Rademacher Judith , Siegert Elise , Radić Mislav , Burmester Gerd-Rüdiger , Dragun Duska , Riemekasten Gabriela 
Published: March 2014

Abstract
Introduction
Agonistic autoantibodies (Aabs) against the angiotensin II receptor type 1 (AT1R) and the endothelin receptor type A (ETAR) have been identified in patients with systemic sclerosis (SSc). In our present study, we examined the expression of the AT1R and the ETAR in human immune cells and the pathological effects mediated through these receptors by their corresponding Aabs.

Methods
Protein expression of AT1R and ETAR on peripheral blood mononuclear cells (PBMCs) from healthy individuals and SSc patients was analyzed using flow cytometry, and mRNA expression of both receptors in PBMCs from healthy donors was examined by real-time PCR. In addition, PBMCs from healthy donors were stimulated in vitro with affinity-purified immunoglobulin G (IgG) fractions from SSc patients positive for AT1R and ETAR Aabs, as well as with IgG from healthy donors serving as controls. Alterations in cell surface marker expression, cytokine secretion and chemotactic motility were analyzed using flow cytometry, enzyme-linked immunosorbent assays and chemotaxis assays, respectively. The results were correlated with the characteristics and clinical findings of the IgG donors.

Results
Both AT1R and ETAR were expressed on PBMCs in humans. Protein expression of both receptors was decreased in SSc patients compared with that of healthy donors and declined during the course of disease. IgG fractions of SSc patients positive for AT1R and ETAR Aabs induced T-cell migration in an Aab level–dependent manner. Moreover, IgG of SSc patients stimulated PBMCs to produce more interleukin 8 (IL-8) and chemokine (C-C motif) ligand 18 (CCL18) than did the IgG of healthy donors. All effects were significantly reduced by selective AT1R and ETAR antagonists. Statistical analysis revealed an association of SSc-IgG induced high IL-8 concentrations with an early disease stage and of high CCL18 concentrations with lung fibrosis onset and vascular complications in the respective IgG donors.

Conclusion
In our present study, we could demonstrate the expression of both AT1R and ETAR on human peripheral T cells, B cells and monocytes. The decreased receptor expression in SSc patients, the inflammatory and profibrotic effects upon Aab stimulation of PBMCs in vitro and the associations with clinical findings suggest a role for Aab-induced activation of immune cells mediated by the AT1R and the ETAR in the pathogenesis or even the onset of the disease.
Inhibitor of DNA binding 1 as a secreted angiogenic transcription factor in rheumatoid arthritis
Authors: Isozaki Takeo , Amin M Asif , Arbab Ali S , Koch Alisa E , Ha Christine M , Edhayan Gautam , Haines G Kenneth , Ruth Jeffrey H 
Published: March 2014

Abstract
Introduction
Rheumatoid arthritis (RA) is characterized by enhanced blood vessel development in joint synovium. This involves the recruitment of endothelial progenitor cells (EPCs), allowing for de novo vessel formation and pro-inflammatory cell infiltration. Inhibitor of DNA Binding 1 (Id1) is a transcription factor characteristic of EPCs that influences cell maturation.

Method
Enzyme-linked immunosorbant assay (ELISA) and polymerase chain reaction (PCR) were used to examine Id1 levels in synovial fluid (SF) and endothelial cells (ECs), respectively. Immunohistology was used to determine the expression of Id1 in synovial tissue (ST). Human dermal microvascular EC (HMVEC) migration and tube forming assays were used to determine if recombinant human Id1 (rhuId1) and/or RA SF immunodepleted Id1 showed angiogenic activity. We also utilized the RA ST severe combined immunodeficient (SCID) mouse chimera to examine if Id1 recruits EPCs to RA synovium.

Results
ST samples immunostained for Id1 showed heightened expression in RA compared to osteoarthritis (OA) and normal (NL) ST. By immunofluorescence staining, we found significantly more Id1 in RA compared to OA and NL vasculature, showing that Id1 expressing cells, and therefore EPCs, are most active in vascular remodeling in the RA synovium. We also detected significantly more Id1 in RA compared to OA and other arthritis SFs by ELISA, which correlates highly with Chemokine (C-X-C motif) ligand 16 (CXCL16) levels. In vitro chemotaxis assays showed that Id1 is highly chemotactic for HMVECs and can be attenuated by inhibition of Nuclear Factor κB and phosphoinositide 3-kinase. Using in vitro Matrigel assays, we found that HMVECs form tubes in response to rhuId1 and that Id1 immunodepleted from RA SF profoundly decreases tube formation in Matrigel in vitro. PCR showed that Id1 mRNA could be up-regulated in EPCs compared to HMVECs in response to CXCL16. Finally, using the K/BxN serum induced arthritis model, we found that EC CXCR6 correlated with Id1 expression by immunohistochemistry.

Conclusions
We conclude that Id1 correlates highly with CXCL16 expression, EPC recruitment, and blood vessel formation in the RA joint, and that Id1 is potently angiogenic and can be up-regulated in EPCs by CXCL16.
The ethical dimension in published animal research in critical care: the dark side of our moon
Authors: Huet Olivier , de Haan Judy B 
Published: March 2014

AbstractThe replacement, refinement, and reduction (3Rs) guidelines are the cornerstone of animal welfare practice for medical research. Nowadays, no animal research can be performed without being approved by an animal ethics committee. Therefore, we should expect that any published article would respect and promote the highest standard of animal welfare. However, in the previous issue of Critical Care, Bara and Joffe reported an unexpected finding: animal welfare is extremely poorly reported in critical care research publications involving animal models. This may have a significant negative impact on the reliability of the results and on future funding for our research. The ability of septic shock animal models to translate into clinical studies has been a challenge. Therefore, every means to improve the quality of these models should be pursued. Animal welfare issues should be seen as an additional benefit to achieve this goal. It is therefore critical to draw conclusions from this study to improve the standard of animal welfare in critical care research. This has already been achieved in other fields of research, and we should follow their example.
Counseling About IUDs: A Mixed‐Methods Analysis
Authors: Dehlendorf Christine , Tharayil Mithu , Anderson Nora , Gbenedio Kessy , Wittman Allen , Steinauer Jody 
Published: March 2014

ContextIUDs are infrequently used in the United States. Assessing how counseling about this method is delivered can help identify barriers to IUD use that might be overcome by improving services.MethodsA sample of 342 family planning visits at six clinics in the San Francisco Bay Area in 2009–2012 were audio‐recorded, and patients completed surveys both before and after their visits. Descriptive quantitative analyses of counseling were performed, and correlates of IUDs’ being mentioned during counseling were investigated using logistic regression. Qualitative analyses investigated the counseling women received about IUDs generally (in a subset of 42 visits), as well as counseling for women who already had an IUD in place (13 visits) or who felt their provider inappropriately expressed a preference for IUDs (five visits).ResultsIUDs were mentioned in 75% of visits. Patient‐initiated mention of IUDs was more likely in visits by women aged 35 or older than in those by women younger than 20 (odds ratio, 6.4); provider‐initiated discussion of this method was less common if the provider was older than 55 than if he or she was younger than 46 (0.3). Providers more often discussed potential adverse effects of IUD use than benefits; counseling often was noninteractive and did not address how patient preferences related to characteristics of IUDs. Counseling was frequently fragmented by the need for return visits or referral elsewhere for insertion.ConclusionsIUD counseling may be improved by enhancing comprehensiveness and patient‐centeredness, and by decreasing fragmentation of care.
Tree regeneration in artificial canopy gaps established for restoring natural structural variability in a Scots pine stand
Authors: Rouvinen Seppo , Kouki Jari 
Published: March 2014

In Finland and elsewhere in Europe, many protected forest areas include also stands that were previously managed and that lack several naturally occurringÂ stand characteristics. In these areas, ecosystem restoration can be used to facilitate and accelerate the formation of structural and habitat features resembling those of natural forests. For example, by creating small gaps it could be possible to diversify forest structure and tree species composition and to produce dead wood while still maintaining mostly continous canopy coverage. We examined experimentally the effects of artificial gap formation on post-disturbance tree regeneration in the gaps in a young protected, but formerly commercially managed pine (Pinus sylvestris L.) dominated forest. In the experimental sites, gap size and the portion of girdled trees out of all treated trees (girdled and felled trees combined) in the gaps varied. Natural and artificial (direct seeding of silver birch Betula pendula Roth) tree regeneration and development was monitored both on disturbed (scarified soil patches) and undisturbed forest floor during three growing seasons. Results show that gaps can be valuable in diversifying stand structure but to be successful and rapid, tree regeneration needs disturbed forest floor. Pine regenerated numerously, but birch had clearly lower regeneration, especially on small-sized gaps. In conclusion, increasing tree diversity in young pine-dominated forests seems to be difficult when only small artificial gaps are used. But even small gaps can be used to create and maintain diverse cohort structure of the dominant species and thus they can contribute to restoration goals.
Polymorphisms in the TLR3 gene are associated with risk for type 1 diabetes mellitus
Authors: Assmann Taís Silveira , Brondani Letícia de Almeida , Bauer Andrea Carla , Canani Luis Henrique , Crispim Daisy 
Published: March 2014

IntroductionViral pathogens seem to play a role in triggering the autoimmune destruction that leads to the development of type 1 diabetes mellitus (T1DM). Toll-like receptor 3 (TLR3) has been shown to recognize double-stranded RNA, a molecular signature of most viruses. It is expressed at high levels in pancreatic β-cells and immune cells, suggesting a role for it in the pathogenesis of T1DM. Therefore, the aim of this study was to investigate whetherTLR3polymorphisms are associated with T1DM.MethodsFrequencies of theTLR3rs11721827, rs13126816, rs5743313, rs7668666, and rs3775291 polymorphisms were analyzed in 449 T1DM patients and in 507 nondiabetic subjects. Haplotypes constructed from the combination of these polymorphisms were inferred using a Bayesian statistical method.ResultsThe rs3775291 and rs13126816 polymorphisms were associated with T1DM, and the strongest association was observed for the additive model (odds ratio (OR)=2.3, 95% CI 1.3–4.2 and OR=2.1, 95% CI 1.3–3.1 respectively). In the same way, the frequency of T1DM was higher as more risk alleles of the five polymorphisms were present (P-trend=0.001). Moreover, in T1DM patients, the minor alleles of the rs5743313 and rs117221827 polymorphisms were associated with an early age at diagnosis and worse glycemic control.ConclusionTheTLR3rs3775291 and rs13126816 polymorphisms are associated with risk for T1DM, while the rs5743313 and rs11721827 polymorphisms are associated with age at T1DM diagnosis and poor glycemic control. The number of risk alleles of the fiveTLR3polymorphisms in the haplotypes seems to influence the risk for T1DM, suggesting that these polymorphisms might interact in the susceptibility for the disease.
Porous Polyimide-Silica Composite: A New Thermal Resistant Flexible Material
Authors: Fukubayashi Yumeto , Yoda Satoshi 
Published: March 2014

ABSTRACTWe developed a new highly porous polyimide (PI) -silica composite with high flexibility, mechanical strength, and heat resistance. The composite was prepared by a new process consisting of (1) phase separation of a mixture of PI precursor (polyamic acid), solvent, and silicon alkoxide, induced by high-pressure CO2 (40 °C, 20 MPa), (2) silicate formation by sol-gel reaction, and (3) supercritical CO2 extraction of the solvent. The composite had a bimodal porous structure with micropores of 10-30 μm and nanopores of ∼50 nm. In the PI matrix, silica nanoparticles (< 100 nm in diameter) were highly dispersed. Porosity of the composite was 78%, which is higher than that of conventional porous PI prepared by physical foaming technique. Relative dielectric constant of the material was lower than 1.4 at 1 MHz. The porous PI-silica composite sheet was flexible enough to be folded without cracking. Notably, the Young’s modulus (0.80 GPa) and the onset decomposition temperature (600 °C) of the PI-silica composite were higher than those of conventional porous PI with similar porosity, respectively. The porous PI-silica composite is promising as a flexible thermal insulator for high-temperature use and as a thermal resistant low-k material.
Resistant to the Recession: Low-Income Adults’ Maintenance of Cooking and Away-From-Home Eating Behaviors During Times of Economic Turbulence
Authors: Smith Lindsey P. , Ng Shu Wen , Popkin Barry M. 
Published: March 2014

Objectives. We examined the effects of state-level unemployment rates during the recession of 2008 on patterns of home food preparation and away-from-home (AFH) eating among low-income and minority populations. Methods. We analyzed pooled cross-sectional data on 118 635 adults aged 18 years or older who took part in the American Time Use Study. Multinomial logistic regression models stratified by gender were used to evaluate the associations between state-level unemployment, poverty, race/ethnicity, and time spent cooking, and log binomial regression was used to assess respondents’ AFH consumption patterns. Results. High state-level unemployment was associated with only trivial increases in respondents’ cooking patterns and virtually no change in their AFH eating patterns. Low-income and racial/ethnic minority groups were not disproportionately affected by the recession. Conclusions. Even during a major economic downturn, US adults are resistant to food-related behavior change. More work is needed to understand whether this reluctance to change is attributable to time limits, lack of knowledge or skill related to food preparation, or lack of access to fresh produce and raw ingredients.