bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of phosphatase of regenerating liver family genes during embryogenesis: an evolutionary developmental analysis among Drosophila, amphioxus, and zebrafish
Authors: Lin Ming-Der , Lee Hsun-Tzu , Wang Szu-Chieh , Li Han-Ru , Hsien Hsin-Lun , Cheng Kai-Wen , Chang Yu-Di , Huang Min-Lang , Yu Jr-Kai , Chen Yau-Hung 
Published: May 2013

Abstract
Background
Phosphatase of regenerating liver (PRL) family is classified as class IVa of protein tyrosine phosphatase (PTP4A) that removes phosphate groups from phosphorylated tyrosine residues on proteins. PRL phosphatases have been implicated in a number of tumorigenesis and metastasis processes and are highly conserved. However, the understanding of PRL expression profiles during embryonic development is very limited.

Results
In this study, we demonstrated and characterized the comprehensive expression pattern of Drosophila PRL, amphioxus PRL, and zebrafish PRLs during embryonic development by either whole mount immunostaining or in situ hybridization. Our results indicate that Drosophila PRL is mainly enriched in developing mid-guts and central nervous system (CNS) in embryogenesis. In amphioxus, initially PRL gene is expressed ubiquitously during early embryogenesis, but its expression become restricted to the anterior neural tube in the cerebral vesicle. In zebrafish, PRL-1 and PRL-2 share similar expression patterns, most of which are neuronal lineages. In contrast, the expression of zebrafish PRL-3 is more specific and preferential in muscle.

Conclusions
This study, for the first time, elucidated the embryonic expression pattern of Drosophila, amphioxus, and zebrafish PRL genes. The shared PRL expression pattern in the developing CNS among diverse animals suggests that PRL may play conserved roles in these animals for CNS development.
A data-driven approach to preprocessing Illumina 450K methylation array data
Authors: Pidsley Ruth , Y Wong Chloe C , Volta Manuela , Lunnon Katie , Mill Jonathan , Schalkwyk Leonard C 
Published: May 2013

Abstract

Background
As the most stable and experimentally accessible epigenetic mark, DNA methylation is of great interest to the research community. The landscape of DNA methylation across tissues, through development and in disease pathogenesis is not yet well characterized. Thus there is a need for rapid and cost effective methods for assessing genome-wide levels of DNA methylation. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a very useful addition to the available methods for DNA methylation analysis but its complex design, incorporating two different assay methods, requires careful consideration. Accordingly, several normalization schemes have been published. We have taken advantage of known DNA methylation patterns associated with genomic imprinting and X-chromosome inactivation (XCI), in addition to the performance of SNP genotyping assays present on the array, to derive three independent metrics which we use to test alternative schemes of correction and normalization. These metrics also have potential utility as quality scores for datasets.

Results
The standard index of DNA methylation at any specific CpG site is β = M/(M + U + 100) where M and U are methylated and unmethylated signal intensities, respectively. Betas (βs) calculated from raw signal intensities (the default GenomeStudio behavior) perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement, even in highly consistent data, by all three metrics. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. More elaborate manipulation of quantiles proves to be counterproductive.

Conclusions
Careful selection of preprocessing steps can minimize variance and thus improve statistical power, especially for the detection of the small absolute DNA methylation changes likely associated with complex disease phenotypes. For the convenience of the research community we have created a user-friendly R software package called wateRmelon, downloadable from bioConductor, compatible with the existing methylumi, minfi and IMA packages, that allows others to utilize the same normalization methods and data quality tests on 450K data.
Temporal changes of cytochrome P450 (Cyp) and eicosanoid-related gene expression in the rat brain after traumatic brain injury
Authors: Birnie Matthew , Morrison Ryan , Camara Ramatoulie , Strauss Kenneth I 
Published: May 2013

AbstractBackgroundTraumatic brain injury (TBI) induces arachidonic acid (ArA) release from cell membranes. ArA metabolites form a class of over 50 bioactive eicosanoids that can induce both adaptive and/or maladaptive brain responses. The dynamic metabolism of ArA to eicosanoids, and how they affect the injured brain, is poorly understood due to their diverse activities, trace levels, and short half-lives. The eicosanoids produced in the brain postinjury depend upon the enzymes present locally at any given time. Eicosanoids are synthesized by heme-containing enzymes, including cyclooxygenases, lipoxygenases, and arachidonate monoxygenases. The latter comprise a subset of the cytochrome P450 “Cyp” gene family that metabolize fatty acids, steroids, as well as endogenous and exogenous toxicants. However, for many of these genes neither baseline neuroanatomical nor injury-related temporal expression have been studied in the brain.In a rat model of parietal cortex TBI,Cypand eicosanoid-related mRNA levels were determined at 6 h, 24 h, 3d, and 7d postinjury in parietal cortex and hippocampus, where dynamic changes in eicosanoids have been observed. Quantitative real-time polymerase chain reaction with low density arrays were used to assay 62 ratCyps, 37 of which metabolize ArA or other unsaturated fatty acids; 16 eicosanoid-related enzymes that metabolize ArA or its metabolites; 8 eicosanoid receptors; 5 other inflammatory- and recovery-related genes, plus 2 mouseCyps as negative controls and 3 highly expressed “housekeeping” genes.ResultsSixteen arachidonate monoxygenases, 17 eicosanoid-related genes, and 12 otherCyps were regulated in the brain postinjury (p < 0.05, Tukey HSD). Discrete tissue levels and distinct postinjury temporal patterns of gene expression were observed in hippocampus and parietal cortex.ConclusionsThe results suggest complex regulation of ArA and other lipid metabolism after TBI. Due to the temporal nature of brain injury-inducedCypgene induction, manipulation of each gene (or its products)at a given time after TBIwill be required to assess their contributions to secondary injury and/or recovery. Moreover, a better understanding of brain region localization and cell type-specific expression may be necessary to deduce the role of these eicosanoid-related genes in the healthy and injured brain.
Fish oil administration in older adults: is there potential for adverse events? A systematic review of the literature
Authors: Villani Anthony M , Crotty Maria , Cleland Leslie G , James Michael J , Fraser Robert J , Cobiac Lynne , Miller Michelle D 
Published: May 2013

Abstract

Background
Omega-3 (n-3) fatty acid supplementation is becoming increasingly popular. However given its antithrombotic properties the potential for severe adverse events (SAE) such as bleeding has safety implications, particularly in an older adult population. A systematic review of randomized control trials (RCT) was conducted to explore the potential for SAE and non-severe adverse events (non-SAE) associated with n-3 supplementation in older adults.

Methods
A comprehensive search strategy using Medline and a variety of other electronic sources was conducted. Studies investigating the oral administration of n-3 fish oil containing eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) or both against a placebo were sourced. The primary outcome of interest included reported SAE associated with n-3 supplementation. Chi-square analyses were conducted on the pooled aggregate of AEs.

Results
Of the 398 citations initially retrieved, a total of 10 studies involving 994 older adults aged ≥60 years were included in the review. Daily fish oil doses ranged from 0.03 g to 1.86 g EPA and/or DHA with study durations ranging from 6 to 52 weeks. No SAE were reported and there were no significant differences in the total AE rate between groups (n-3 intervention group: 53/540; 9.8%; placebo group: 28/454; 6.2%; p = 0.07). Non-SAE relating to gastrointestinal (GI) disturbances were the most commonly reported however there was no significant increase in the proportion of GI disturbances reported in participants randomized to the n-3 intervention (n-3 intervention group: 42/540 (7.8%); placebo group: 24/454 (5.3%); p = 0.18).

Conclusions
The potential for AEs appear mild-moderate at worst and are unlikely to be of clinical significance. The use of n-3 fatty acids and the potential for SAE should however be further researched to investigate whether this evidence is consistent at higher doses and in other populations. These results also highlight that well-documented data outlining the potential for SAE following n-3 supplementation are limited nor adequately reported to draw definitive conclusions concerning the safety associated with n-3 supplementation. A more rigorous and systematic approach for monitoring and recording AE data in clinical settings that involve n-3 supplementation is required.
Plasma metabolomics identifies lipid abnormalities linked to markers of inflammation, microbial translocation, and hepatic function in HIV patients receiving protease inhibitors
Authors: Cassol Edana , Misra Vikas , Holman Alexander , Kamat Anupa , Morgello Susan , Gabuzda Dana 
Published: May 2013

AbstractBackgroundMetabolic abnormalities are common in HIV-infected individuals on antiretroviral therapy (ART), but the biochemical details and underlying mechanisms of these disorders have not been defined.MethodsUntargeted metabolomic profiling of plasma was performed for 32 HIV patients with low nadir CD4 counts (<300 cells/ul) on protease inhibitor (PI)-based ART and 20 healthy controls using liquid or gas chromatography and mass spectrometry. Effects of Hepatitis C (HCV) co-infection and relationships between altered lipid metabolites and markers of inflammation, microbial translocation, and hepatic function were examined. Unsupervised hierarchical clustering, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), Random forest, pathway mapping, and metabolite set enrichment analysis (MSEA) were performed using dChip, Metaboanalyst, and MSEA software.ResultsA 35-metabolite signature mapping to lipid, amino acid, and nucleotide metabolism distinguished HIV patients with advanced disease on PI-based ART from controls regardless of HCV serostatus (p<0.05, false discovery rate (FDR)<0.1). Many altered lipids, including bile acids, sulfated steroids, polyunsaturated fatty acids, and eicosanoids, were ligands of nuclear receptors that regulate metabolism and inflammation. Distinct clusters of altered lipids correlated with markers of inflammation (interferon-α and interleukin-6), microbial translocation (lipopolysaccharide (LPS) and LPS-binding protein), and hepatic function (bilirubin) (p<0.05). Lipid alterations showed substantial overlap with those reported in non-alcoholic fatty liver disease (NALFD). Increased bile acids were associated with noninvasive markers of hepatic fibrosis (FIB-4, APRI, and YKL-40) and correlated with acylcarnitines, a marker of mitochondrial dysfunction.ConclusionsLipid alterations in HIV patients receiving PI-based ART are linked to markers of inflammation, microbial translocation, and hepatic function, suggesting that therapeutic strategies attenuating dysregulated innate immune activation and hepatic dysfunction may be beneficial for prevention and treatment of metabolic disorders in HIV patients.
Rapid-developed primary malignant myoepithelioma in the cavernous sinus: a case report
Authors: Hong Yuan , Guo Song-Xue , Chen Sheng , Klebe Damon , Zhang Jian-Min , Wu Qun 
Published: May 2013

Abstract

Background
Malignant myoepithelioma is a relatively rare malignant tumor occurring most frequently in the salivary glands. A few isolated cases have been described in other locations, including soft tissue, bone, lung, bronchus, oral cavity, nasopharynx, larynx, and maxillary sinus. Malignant myoepithelioma, however, is uncommonly involved within the cavernous sinus. To the best of our knowledge, this is the first report of malignant myoepithelioma arising from within the cavernous sinus.

Case presentation
Herein, we report a case of a 48-year-old woman who presented a 1-month history of diplopia and blepharoptosis as well as radiological evidence of a rapidly developing cavernous sinus tumor. The patient underwent a trans-sphenoidal biopsy and a histological diagnosis indicated a malignant myoepithelioma. After diagnosis, the tumor grew rapidly and her clinical condition deteriorated progressively. Therefore, a pterional craniotomy with partial tumor removal was performed. The patient’s clinical state was worsened, and she died two months after the initial operation. Because the malignant myoepithelioma could not be traced to an organ of origin, other than the cavernous sinus, this case was diagnosed as a primary intracranial malignant myoepithelioma.

Conclusion
The purpose of presenting this case report is to raise awareness among clinicians to consider malignant myoepithelioma as a differential diagnosis when a cavernous sinus mass is identified. Furthermore, an ideal management strategy for malignant myoepithelioma is not known and the prognosis seems to be unfavorable; therefore, more cases are needed to enhance our knowledge of the diagnosis, treatment, and prognosis of this rare intracranial lesion.
Imatinib mesylate inhibits cell growth of malignant peripheral nerve sheath tumors in vitro and in vivothrough suppression of PDGFR-β
Authors: Ohishi Jun , Aoki Mikiko , Nabeshima Kazuki , Suzumiya Junji , Takeuchi Tamotsu , Ogose Akira , Hakozaki Michiyuki , Yamashita Yuichi , Iwasaki Hiroshi 
Published: May 2013

Abstract

Background
Malignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive and associated with poor prognosis. Basic research to develop new treatment regimens is critically needed.

Methods
The effects of imatinib mesylate on MPNSTs were examined in six human MPNST cell lines and in a xenograft mouse model.

Results
The results showed expression of platelet-derived growth factor receptor-β and suppression of its phosphorylation by imatinib mesylate in all six cell lines. Imatinib mesylate effectively suppressed MPNST cell growth in vitro at concentrations similar to those used clinically (1.46 − 4.6 μM) in three of six cell lines. Knockdown of PDGFR-β by transfection with a specific siRNA also caused significant reduction in cell proliferation in the sensitive cell lines, but not in the resistant cell lines. Furthermore, imatinib mesylate also significantly suppressed colony formation within soft agar and tumor growth in xenograft models using two of the three sensitive MPNST cell lines. There was excellent agreement between in vitro and in vivo sensitivity to imatinib mesylate, suggesting possible selection of imatinib-sensitive tumors by in vitro analysis.

Conclusions
The results suggest that imatinib mesylate may be useful in the treatment of MPNST patients and in vitro studies may help select cells that are sensitive to imatinib mesylate in vivo.
Antilock braking system effectiveness in prevention of road traffic crashes in Iran
Authors: Khorasani-Zavareh Davoud , Shoar Saeed , Saadat Soheil 
Published: May 2013

Abstract

Background
Anti-lock Brake System (ABS) helps the equipped vehicles to stop under heavy braking, in a shorter distance and with a better control of direction. It was expected that this technology will reduce the rate of fatal road traffic crashes (RTC); however, the outcome is controversial in the real world. The aim of this study is to compare the claimed annual incidence rate and financial losses due to RTCs in ABS vs. non-ABS personal vehicles in Iran.

Methods
A telephone survey among drivers of two similar models of personal vehicles was arranged. The studied vehicles were of the same brand and type; but only one of them was equipped with ABS. The number of RTCs, subsequent financial loss, and drivers’ knowledge and perception about ABS were sought. The sample consisted of drivers of 1232 ABS and 3123 non-ABS vehicles.

Results
The annual incidence rate of RTC involving another vehicle was 145.1 (134.8-155.9) per 1000 vehicle-years and there was not a statistically significant difference between study groups.
The incidence of RTC with another vehicle due to brake failure was 50.3 (42.9-58.5) for 1000 non ABS vehicle-years and 30.0 (21.2-41.2) for 1000 ABS equipped vehicle-years. The difference was statistically significant after adjustment for the driver and vehicle's age and the daily driving time. The attributable risk of RTC for non-ABS vehicles was 20/1000 vehicles and the excess fraction was 39.8%. The mean financial loss due to reported RTCs was $987.9 ± $1547.3 US Dollars and there was not a statistically significant difference between study groups. While 61.1% of ABS vehicle drivers reported situations in which they believed the ABS had prevented a crash, 44.1% of them however, they did not know how to use ABS efficiently.

Conclusions
Law enforcement to maintain safe distance and adhere to speed limit while driving, is needed to raise the effectiveness of ABS. This is as necessary as considering mandatory outfitting of ABS. Safety authorities should first consider the global experience and local evidence, before adopting any specific policy in this regard. The drivers need to learn the right way to use ABS for maximum effectiveness.
Daily temperature fluctuations unpredictably influence developmental rate and morphology at a critical early larval stage in a frog
Authors: Arrighi Juliana M , Lencer Ezra S , Jukar Advait , Park Daesik , Phillips Patrick C , Kaplan Robert H 
Published: May 2013

AbstractBackgroundEnvironmental temperature has profound consequences for early amphibian development and many field and laboratory studies have examined this. Most laboratory studies that have characterized the influence of temperature on development in amphibians have failed to incorporate the realities of diel temperature fluctuations (DTF), which can be considerable for pond-breeding amphibians.ResultsWe evaluated the effects of different ecologically relevant ranges of DTF compared with effects of constant temperatures on development of embryos and larvae of the Korean fire-bellied toad (Bombina orientalis). We constructed thermal reaction norms for developmental stage, snout- vent length, and tail length by fitting a Gompertz-Gaussian function to measurements taken from embryos after 66 hours of development in 12 different constant temperature environments between 14°C and 36°C. We used these reaction norms as null models to test the hypothesis that developmental effects of DTF are more than the sum of average constant temperature effects over the distribution of temperatures experienced. We predicted from these models that growth and differentiation would be positively correlated with average temperature at low levels of DTF but not at higher levels of DTF. We tested our prediction in the laboratory by rearingB. orientalisembryos at three average temperatures (20°C, 24°C, and 28°C) and four levels of thermal variation (0°C, 6°C, 13°C, and 20°C). Several of the observed responses to DTF were significantly different from both predictions of the model and from responses in constant temperature treatments at the same average temperatures. At an average temperature of 24°C, only the highest level of DTF affected differentiation and growth rates, but at both cooler and warmer average temperatures, moderate DTF was enough to slow developmental and tail growth rates.ConclusionsThese results demonstrate that both the magnitude of DTF range and thermal averages need to be considered simultaneously when parsing the effects of changing thermal environments on complex developmental responses, particularly when they have potential functional and adaptive significance.
Factors that influence midwifery students in Ghana when deciding where to practice: a discrete choice experiment
Authors: Ageyi-Baffour Peter , Rominski Sarah , Nakua Emmanuel , Gyakobo Mawuli , Lori Jody R 
Published: May 2013

Abstract

Background
Mal-distribution of the health workforce with a strong bias for urban living is a major constraint to expanding midwifery services in Ghana. According to the UN Millennium Development Goals (MDG) report, the high risk of dying in pregnancy or childbirth continues in Africa. Maternal death is currently estimated at 350 per 100,000, partially a reflection of the low rates of professional support during birth. Many women in rural areas of Ghana give birth alone or with a non-skilled attendant. Midwives are key healthcare providers in achieving the MDGs, specifically in reducing maternal mortality by three-quarters and reducing by two-thirds the under 5 child mortality rate by 2015.

Methods
This quantitative research study used a computerized structured survey containing a discrete choice experiment (DCE) to quantify the importance of different incentives and policies to encourage service to deprived, rural and remote areas by upper-year midwifery students following graduation. Using a hierarchical Bayes procedure we estimated individual and mean utility parameters for two hundred and ninety eight third year midwifery students from two of the largest midwifery training schools in Ghana.

Results
Midwifery students in our sample identified: 1) study leave after two years of rural service; 2) an advanced work environment with reliable electricity, appropriate technology and a constant drug supply; and 3) superior housing (2 bedroom, 1 bathroom, kitchen, living room, not shared) as the top three motivating factors to accept a rural posting.

Conclusion
Addressing the motivating factors for rural postings among midwifery students who are about to graduate and enter the workforce could significantly contribute to the current mal-distribution of the health workforce.