bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression profiling of genes regulated by Fra-1/AP-1 transcription factor during bleomycin-induced pulmonary fibrosis
Authors: Rajasekaran Subbiah , Reddy Narsa M , Zhang Wei , Reddy Sekhar P 
Published: June 2013

AbstractBackgroundThe Fra-1/AP-1 transcription factor regulates the expression of genes controlling various processes including migration, invasion, and survival as well as extracellular remodeling. We recently demonstrated that loss ofFra-1leads to exacerbated bleomycin-induced pulmonary fibrosis, accompanied by enhanced expression of various inflammatory and fibrotic genes. To better understand the molecular mechanisms by which Fra-1 confers protection during bleomycin-induced lung injury, genome-wide mRNA expression profiling was performed.ResultsWe found that Fra-1 regulates gene expression programs that include: 1) several cytokines and chemokines involved in inflammation, 2) several genes involved in the extracellular remodeling and cell adhesion, and 3) several genes involved in programmed cell death.ConclusionLoss of Fra-1 leads to the enhanced expression of genes regulating inflammation and immune responses and decreased the expression of genes involved in apoptosis, suggesting that this transcription factor distinctly modulates early pro-fibrotic cellular responses.
Detection of selective sweeps in cattle using genome-wide SNP data
Authors: Ramey Holly R , Decker Jared E , McKay Stephanie D , Rolf Megan M , Schnabel Robert D , Taylor Jeremy F 
Published: June 2013

AbstractBackgroundThe domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Selective sweeps have now been identified in the genomes of many animal species including humans, dogs, horses, and chickens. Here, we attempt to identify and characterise regions of the bovine genome that have been subjected to selective sweeps.ResultsTwo datasets were used for the discovery and validation of selective sweeps via the fixation of alleles at a series of contiguous SNP loci. BovineSNP50 data were used to identify 28 putative sweep regions among 14 diverse cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 85 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions and the lack of sequence data for the analysed breeds precludes the nomination of selected genes or variants and limits the prediction of the selected phenotypes. However, phenotypes that we predict to have historically been under strong selection include horned-polled, coat colour, stature, ear morphology, and behaviour.ConclusionsThe bias towards common SNPs in the design of the BovineSNP50 assay led to the identification of recent selective sweeps associated with breed formation and common to only a small number of breeds rather than ancient events associated with domestication which could potentially be common to all European taurines. The limited SNP density, or marker resolution, of the BovineSNP50 assay significantly impacted the rate of false discovery of selective sweeps, however, we found sweeps in common between breeds which were confirmed using an ultra-high-density assay scored in a small number of animals from a subset of the breeds. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories and the very different environmental habitats to which these sub-species have adapted.
Integrating nurse-led Self-Management Support (SMS) in routine primary care: design of a hybrid effectiveness-implementation study among type 2 diabetes patients with problems of daily functioning and emotional distress: a study protocol
Authors: van Dijk - de Vries Anneke , van Bokhoven Marloes A , Terluin Berend , van der Weijden Trudy , van Eijk Jacques Th M 
Published: June 2013

Abstract

Background
Psychosocial problems are more prevalent among patients with chronic diseases than among the general population. They may lead to a downward spiral of poor adherence, deterioration of the condition and decline in daily functioning. In addition to medical management, systematic attention to emotional and role management tasks during routine chronic care seems mandatory. We intend to integrate an existing nurse-led minimal psychological intervention to support patients’ self-management, which appeared to be effective and cost-effective, in routine care by primary care nurses, so we adjusted it to fit the host setting. The resulting Self-Management Support (SMS) programme involves early detection of patients with emotional distress and problems of daily functioning, as well as self-management support through problem solving and reattribution techniques. Strategies to embed SMS in daily practice include training and booster sessions for practice nurses as well as organisational and financial arrangements. This study aims to simultaneously evaluate the implementation process and effects of SMS in routine care, using a hybrid effectiveness–implementation design.

Methods/Design
Registration data, questionnaires and interviews will be used to explore the facilitators, barriers and costs regarding successful implementation of SMS. The effects of SMS will be evaluated in a pragmatic cluster-randomised controlled trial with a baseline measurement and follow-up measurements after 4 and 12 months. The population will consist of 46 practice nurses and their type 2 diabetes patients (N = 460; 10 per practice nurse). The practice nurses will be randomly assigned to the intervention or control group. Practice nurses of the intervention group will receive SMS training. Patients for the intervention and control groups will be recruited by a researcher-led self-administered screening procedure to decide which patients of those scheduled for routine consultation are likely to be detected by the practice nurses as eligible for the self-management support. Primary outcome measure is patients’ daily functioning. Secondary measures include emotional well-being, participation, autonomy and control over the disease.

Discussion
Our hybrid study design is complicated by the detection method used by the practice nurses. This method is an implementation issue in itself that has consequences for the realisation and power of the effect evaluation.

Trial registration
Current Controlled Trials, NTR2764
Epidemiology of hepatitis B and hepatitis C virus infections in pregnant women in Sana’a, Yemen
Authors: Murad Entisar A , Babiker Suad M , Gasim Gasim I , Rayis Duria A , Adam Ishag 
Published: June 2013

Abstract

Background
Screening for Hepatitis B and C during pregnancy may help to decide on appropriate antiviral therapy and the institution of steps to minimize vertical transmission to the newborn infants.

Methods
A cross-sectional study was conducted during November–December 2011 to investigate the seroprevalence and associated risk factors for markers of HBV (hepatitis B surface antigen; HBsAg) and anti-HCV antibody among pregnant women at the Al-Thawra hospital in Sana’a, Yemen. Structured questionnaires were used to obtain sociodemographic obstetrics and medical data and sera were tested for HBsAg and anti-HCV.

Results
Of the 400 pregnant women enrolled in the study, HBsAg and anti-HCV were detected in 43 (10.8%; 95% CI: 8.0–14.0%) and 34 (8.5%, 95% CI: 6.0–11.5%) women, respectively. None of the women were co-infected with HBV and HCV. Multivariate analysis showed that circumcision was significantly associated with HBsAg seropositivity (OR = 3.3, 95% CI: 1.1–10.2; p = 0.03), low parity (primigravidae and secundigravidae) and education below secondary level were significantly associated with anti- HCV seropositivity (OR = 3.3, 95% CI: 1.1–10.2; p = 0.03). No other sociodemographic or clinical characteristics (age, residence, history of home delivery, miscarriage, dental manipulation, surgery, and blood transfusion) were significantly associated with HBsAg or anti-HCV seropositivity.

Conclusion
The results of this study suggest that HBsAg and anti-HCV have high prevalence among pregnant women.
Effect of an isoenergetic traditional Mediterranean diet on apolipoprotein A-I kinetic in men with metabolic syndrome
Authors: Richard Caroline , Couture Patrick , Desroches Sophie , Lichtenstein Alice H , Lamarche Benoît 
Published: June 2013

Abstract

Background
The impact of the Mediterranean diet (MedDiet) on high-density lipoprotein (HDL) kinetics has not been studied to date. The objective of this study was therefore to investigate the effect of the MedDiet in the absence of changes in body weight on apolipoprotein (apo) A-I kinetic in men with metabolic syndrome (MetS).

Methods
Twenty-six men with MetS (NCEP-ATP III) were recruited from the general community. In this fixed sequence study, participants’ diet was first standardized to a control diet reflecting current averages in macronutrient intake in North American men, with all foods and beverages provided under isoenergetic conditions for 5 weeks. Participants were then fed an isoenergetic MedDiet over a subsequent period of 5 weeks to maintain their weight constant. During the last week of each diet, participants received a single bolus dose of [5,5,5-2H3] L-leucine and fasting blood samples were collected at predetermined time points. ApoA-I kinetic was determined by multicompartmental modeling using isotopic enrichment data over time. Data were analyses using MIXED models.

Results
The response of HDL-cholesterol (C) to MedDiet was heterogeneous, such that there was no mean change compared with the control diet. Plasma apoA-I concentration (−3.9%) and pool size (−5.3%, both P < 0.05) were significantly lower after MedDiet and apoA-I production rate tended to be reduced (−5.7%, P = 0.07) with no change in apoA-I fractional catabolic rate (FCR, -1.6%, P = 0.64). Participants among whom HDL-C concentrations were increased with MedDiet (responders: mean ∆HDL-C: +9.9 ± 3.2%, N = 11) showed significantly greater reductions in apoA-I FCR and in apoB and very-low-density lipoprotein-triglycerides (VLDL-TG) concentrations (all P < 0.04) than those among whom HDL-C levels were reduced after the MedDiet (non-responders: mean ∆HDL-C: -12.0 ± 3.9%, N = 8). Correlation analysis revealed that only variations in apoA-I FCR (r = -0.48, P = 0.01) and in plasma VLDL-TG (r = −0.45, P = 0.03) concentrations were correlated with the individual HDL-C response to the MedDiet.

Conclusions
Data from this controlled feeding study suggest that the heterogeneous response of HDL-C to MedDiet, in the absence of important weight loss, is primarily related to individual variations in apoA-I FCR and in plasma VLDL-TG concentrations.

Trial registration
ClinicalTrial.gov registration number: NCT00988650
An observational study reveals that neonatal vitamin D is primarily determined by maternal contributions: implications of a new assay on the roles of vitamin D forms
Authors: Karras Spyridon N , Shah Iltaf , Petroczi Andrea , Goulis Dimitrios G , Bili Helen , Papadopoulou Fotini , Harizopoulou Vikentia , Tarlatzis Basil C , Naughton Declan P 
Published: June 2013

Abstract

Background
Vitamin D concentrations during pregnancy are measured to diagnose states of insufficiency or deficiency. The aim of this study is to apply accurate assays of vitamin D forms [single- hydroxylated [25(OH)D2, 25(OH)D3], double-hydroxylated [1α,25(OH)2D2, 1α,25(OH)2D3], epimers [3-epi-25(OH)D2, 3-epi-25(OH)D3] in mothers (serum) and neonates (umbilical cord) to i) explore maternal and neonatal vitamin D biodynamics and ii) to identify maternal predictors of neonatal vitamin D concentrations.

Methods
All vitamin D forms were quantified in 60 mother- neonate paired samples by a novel liquid chromatography -mass spectrometry (LC-MS/MS) assay. Maternal characteristics [age, ultraviolet B exposure, dietary vitamin D intake, calcium, phosphorus and parathyroid hormone] were recorded. Hierarchical linear regression was used to predict neonatal 25(OH)D concentrations.

Results
Mothers had similar concentrations of 25(OH)D2 and 25(OH)D3 forms compared to neonates (17.9 ± 13.2 vs. 15.9 ± 13.6 ng/mL, p = 0.289) with a ratio of 1:3. The epimer concentrations, which contribute approximately 25% to the total vitamin D levels, were similar in mothers and neonates (4.8 ± 7.8 vs. 4.5 ± 4.7 ng/mL, p = 0.556). No correlation was observed in mothers between the levels of the circulating form (25OHD3) and its active form. Neonatal 25(OH)D2 was best predicted by maternal characteristics, whereas 25(OH)D3 was strongly associated to maternal vitamin D forms (R2 = 0.253 vs. 0.076 and R2 = 0.109 vs. 0.478, respectively). Maternal characteristics explained 12.2% of the neonatal 25(OH)D, maternal 25(OH)D concentrations explained 32.1%, while epimers contributed an additional 11.9%.

Conclusions
By applying a novel highly specific vitamin D assay, the present study is the first to quantify 3-epi-25(OH)D concentrations in mother - newborn pairs. This accurate assay highlights a considerable proportion of vitamin D exists as epimers and a lack of correlation between the circulating and active forms. These results highlight the need for accurate measurements to appraise vitamin D status. Maternal characteristics and circulating forms of vitamin D, along with their epimers explain 56% of neonate vitamin D concentrations. The roles of active and epimer forms in the maternal - neonatal vitamin D relationship warrant further investigation.
GP73 is down-regulated in gastric cancer and associated with tumor differentiation
Authors: Chen Le-Gao , Wang Hui-Ju , Yao Hai-bo , Guan Tian-Pei , Wu Fang , He Xu-Jun , Ma Ying-Yu , Tao Hou-Quan , Ye Zai-Yuan 
Published: June 2013

Abstract

Background
Golgi protein 73 (GP73) is a type II Golgi transmembrane protein. It is over-expressed in several cancers, including hepatocellular carcinomas, bile duct carcinomas, lung cancer and prostate cancer. However, there are few reports of GP73 in gastric cancer. This study is aimed at investigating the expression of GP73 and its relationship with clinical pathological characters in gastric cancer.

Methods
GP73 mRNA level was determined by quantitative real-time RT-PCR in 41 pairs of matched gastric tumorous tissues and adjacent non-tumorous mucosal tissues. Western blotting was also performed to detect the GP73 protein level. GP73 protein expression was analyzed by immunohistochemistry in 52 clinically characterized gastric cancer patients and 10 non-tumorous gastric mucosal tissue controls.

Results
The mRNA and protein level of GP73 were significantly down-regulated in gastric tumorous tissues compared with the non-tumorous mucosal tissues. In non-tumorous mucosa, strong diffuse cytoplasmic staining can be seen in cells located at the surface of the glandular and foveolar compartment; while in tumorous tissues, the staining was much weaker or even absent, and mainly in a semi-granular dot-like staining pattern. The expression level of GP73 protein was associated with patients’ gender and tumor differentiation.

Conclusions
GP73 was normally expressed in non-tumorous gastric mucosa and down-regulated in gastric cancer. Its expression in gastric cancer was correlated with tumor differentiation.
Surface roughness effects on the frequency tuning performance of a nanoelectromechanical resonator
Authors: Yoon Hyong Seo , Park Byeongho , Jun Seong Chan 
Published: June 2013

Abstract
Electrothermal heating is one of radio frequency tuning method in nanoelectromechanical resonators with magnetomotive transduction. This study confirmed that the surface roughness of the nanoresonator affects the electrothermal tuning performance under moderate conditions at room temperature. The effect of surface roughness on electrothermal tuning is complicated and involves interactions of mechanical and electrical properties. In addition, the electrothermal damping varied depending on the nanoscale molecular solid structure. These factors affect the signal-to-noise ratio, the effective stress of the beam, and the quality Q-factor of the nanoresonator.
Spatial resolution of confocal XRF technique using capillary optics
Authors: Dehlinger Maël , Fauquet Carole , Lavandier Sebastien , Aumporn Orawan , Jandard Franck , Arkadiev Vladimir , Bjeoumikhov Aniouar , Tonneau Didier 
Published: June 2013

Abstract
XRF (X-ray fluorescence) is a powerful technique for elemental analysis with a high sensitivity. The resolution is presently limited by the size of the primary excitation X-ray beam. A test-bed for confocal-type XRF has been developed to estimate the ultimate lateral resolution which could be reached in chemical mapping using this technique. A polycapillary lens is used to tightly focus the primary X-ray beam of a low power rhodium X-ray source, while the fluorescence signal is collected by a SDD detector through a cylindrical monocapillary. This system was used to characterize the geometry of the fluorescent zone. Capillary radii ranging from 50 μm down to 5 μm were used to investigate the fluorescence signal maximum level This study allows to estimate the ultimate resolution which could be reached in-lab or on a synchrotron beamline. A new tool combining local XRF and scanning probe microscopy is finally proposed.
Absolute flatness measurements of silicon mirrors by a three-intersection method by near-infrared interferometry
Authors: Uchikoshi Junichi , Hayashi Yoshinori , Ajari Noritaka , Kawai Kentaro , Arima Kenta , Morita Mizuho 
Published: June 2013

Abstract
Absolute flatness of three silicon plane mirrors have been measured by a three-intersection method based on the three-flat method using a near-infrared interferometer. The interferometer was constructed using a near-infrared laser diode with a 1,310-nm wavelength light where the silicon plane mirror is transparent. The height differences at the coordinate values between the absolute line profiles by the three-intersection method have been evaluated. The height differences of the three flats were 4.5 nm or less. The three-intersection method using the near-infrared interferometer was useful for measuring the absolute flatness of the silicon plane mirrors.
A cost effective real-time PCR for the detection of adenovirus from viral swabs
Authors: Al-Siyabi Turkiya , Binkhamis Khalifa , Wilcox Melanie , Wong Sallene , Pabbaraju Kanti , Tellier Raymond , Hatchette Todd F , LeBlanc Jason J 
Published: June 2013

Abstract
Compared to traditional testing strategies, nucleic acid amplification tests such as real-time PCR offer many advantages for the detection of human adenoviruses. However, commercial assays are expensive and cost prohibitive for many clinical laboratories. To overcome fiscal challenges, a cost effective strategy was developed using a combination of homogenization and heat treatment with an “in-house” real-time PCR. In 196 swabs submitted for adenovirus detection, this crude extraction method showed performance characteristics equivalent to viral DNA obtained from a commercial nucleic acid extraction. In addition, the in-house real-time PCR outperformed traditional testing strategies using virus culture, with sensitivities of 100% and 69.2%, respectively. Overall, the combination of homogenization and heat treatment with a sensitive in-house real-time PCR provides accurate results at a cost comparable to viral culture.
Cytoplasmic RNA viruses as potential vehicles for the delivery of therapeutic small RNAs
Authors: Usme-Ciro Jose A , Campillo-Pedroza Natalia , Almazán Fernando , Gallego-Gomez Juan C 
Published: June 2013

Abstract
Viral vectors have become the best option for the delivery of therapeutic genes in conventional and RNA interference-based gene therapies. The current viral vectors for the delivery of small regulatory RNAs are based on DNA viruses and retroviruses/lentiviruses. Cytoplasmic RNA viruses have been excluded as viral vectors for RNAi therapy because of the nuclear localization of the microprocessor complex and the potential degradation of the viral RNA genome during the excision of any virus-encoded pre-microRNAs. However, in the last few years, the presence of several species of small RNAs (e.g., virus-derived small interfering RNAs, virus-derived short RNAs, and unusually small RNAs) in animals and cell cultures that are infected with cytoplasmic RNA viruses has suggested the existence of a non-canonical mechanism of microRNA biogenesis. Several studies have been conducted on the tick-borne encephalitis virus and on the Sindbis virus in which microRNA precursors were artificially incorporated and demonstrated the production of mature microRNAs. The ability of these viruses to recruit Drosha to the cytoplasm during infection resulted in the efficient processing of virus-encoded microRNA without the viral genome entering the nucleus. In this review, we discuss the relevance of these findings with an emphasis on the potential use of cytoplasmic RNA viruses as vehicles for the efficient delivery of therapeutic small RNAs.
Placental DNA hypomethylation in association with particulate air pollution in early life
Authors: Janssen Bram G , Godderis Lode , Pieters Nicky , Poels Katrien , Kiciński Michał , Cuypers Ann , Fierens Frans , Penders Joris , Plusquin Michelle , Gyselaers Wilfried , Nawrot Tim S 
Published: June 2013

Abstract

Background
There is evidence that altered DNA methylation is an important epigenetic mechanism in prenatal programming and that developmental periods are sensitive to environmental stressors. We hypothesized that exposure to fine particles (PM2.5) during pregnancy could influence DNA methylation patterns of the placenta.

Methods
In the ENVIRON AGE birth cohort, levels of 5’-methyl-deoxycytidine (5-mdC) and deoxycytidine (dC) were quantified in placental DNA from 240 newborns. Multiple regression models were used to study placental global DNA methylation and in utero exposure to PM2.5 over various time windows during pregnancy.

Results
PM2.5 exposure during pregnancy averaged (25th-75th percentile) 17.4 (15.4-19.3) μg/m3. Placental global DNA methylation was inversely associated with PM2.5 exposures during whole pregnancy and relatively decreased by 2.19% (95% confidence interval [CI]: -3.65, -0.73%, p = 0.004) for each 5 μg/m3 increase in exposure to PM2.5. In a multi-lag model in which all three trimester exposures were fitted as independent variables in the same regression model, only exposure to PM2.5 during trimester 1 was significantly associated with lower global DNA methylation (-2.13% per 5 μg/m3 increase, 95% CI: -3.71, -0.54%, p = 0.009). When we analyzed shorter time windows of exposure within trimester 1, we observed a lower placental DNA methylation at birth during all implantation stages but exposure during the implantation range (6-21d) was strongest associated (-1.08% per 5 μg/m3 increase, 95% CI: -1.80, -0.36%, p = 0.004).

Conclusions
We observed a lower degree of placental global DNA methylation in association with exposure to particulate air pollution in early pregnancy, including the critical stages of implantation. Future studies should elucidate genome-wide and gene-specific methylation patterns in placental tissue that could link particulate exposure during in utero life and early epigenetic modulations.