bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of duodenojejunal flexure formation in mice: implications for understanding the genetic basis for gastrointestinal morphology in mammals
Authors: Onouchi Sawa , Ichii Osamu , Otsuka Saori , Hashimoto Yoshiharu , Kon Yasuhiro 
Published: August 2013

AbstractThe mammalian gut undergoes morphological changes during development. We studied the developing mouse duodenojejunal flexure (DJF) to elucidate the mechanism of formation. During embryonic days 10.75–13.75, DJF formation was morphologically classified into three stages: the expansion stage, flexure formation stage, and flexure elongation stage. From the expansion to the flexure formation stages, the DJF wall showed asymmetric morphology and proliferation along the left‐right intestinal axis. From the flexure formation to the flexure elongation stage, the DJF started to bend dorsally with counterclockwise rotation along the antero‐caudal intestinal axis, indicating that the original right side of the duodenum was rotated towards the dorsal body wall during development of the DJF. The direction of attachment of the dorsal mesentery to the DJF did not correspond to the bending direction of the DJF during flexure formation, and this finding indicated that the dorsal mesentery contributed very little to DJF formation. During DJF formation, Aldh1a2 and hedgehog mRNAs were detected at the DJF, and their expression levels differed along the bending axis. In conclusion, DJF formation might be triggered by asymmetric morphology and proliferation along the left‐right intestinal axis under the control of retinoic acid and hedgehog signaling.
Long‐Term Follow‐Up of Coronary Venous Bypass Graft Lesions Treated with a New Generation Drug‐Eluting Stent with Bioabsorbable Polymer
Authors: WESSELY RAINER , MARZOCCHI ANTONIO , SCHWACKE HARALD , BERTEL OSMUND , LAANMETS PEEP , PERISIC ZORAN , TOELG RALPH , JAGIC NIKOLA , ELSÄSSER ALBRECHT , DANZI GIAN BATTISTA 
Published: August 2013

AbstractBackgroundTo date, no published data are available regarding long‐term follow‐up of new generation DES implanted in coronary artery bypass graft (CABG) lesions.ObjectivesTo assess the long‐term clinical outcome of patients receiving the new generation Biolimus A9‐coated drug‐eluting stent (DES) with biodegradable polymer in saphenous vein grafts (SVG).MethodsThree thousand sixty‐seven patients were included in the NOBORI 2 registry: 71 patients with a total of 117 lesions received at least 1 biolimus A9 DES in SVG lesions and 2,959 patients received percutaneous coronary intervention in other lesions. Clinical follow‐up was performed at 1, 6, and 12 months, and annually up to 3 years.ResultsCompared to the non‐CABG group, patients with CABG lesions were older (P < 0.001), had a higher Charlson Comorbidity Index (P = 0.004), and presented more often with acute coronary syndrome (P = 0.02). At 3‐year follow‐up, cardiac death occurred in 9.7% versus 2.1% (P < 0.001), myocardial infarction (MI) in 8.3% versus 3.0% (P = 0.02), target lesion failure in 13.9% versus 6.4% (P = 0.03), and major adverse cardiac event in 18.1% versus 8.6% (P = 0.01). No differences were observed in TV‐MI and TLR, nor stent thrombosis (ST) which was generally low in both groups (1.4% vs 0.8%, P = NS).ConclusionAlbeit 3‐year outcomes were less favorable in the CABG group, the higher cardiac mortality was apparently not driven by ST, target vessel MI, or TLR, but is likely due to advanced disease and age as well as comorbidity. The low TLR rate as well as the absence of late and very late ST suggest that BES are safe and effective for the treatment of CABG lesions. (J Interven Cardiol 2013;26:425‐433)
Mycobacterium bovis BCG killed by extended freeze‐drying induces an immunoregulatory profile and protects against atherosclerosis
Authors: Ovchinnikova O. A. , Berge N. , Kang C. , Urien C. , Ketelhuth D. F. J. , Pottier J. , Drouet L. , Hansson G. K. , Marchal G. , Bäck M. , Schwartz‐Cornil I. , Lagranderie M. 
Published: August 2013

AbstractObjectivesAtherosclerosis is an inflammatory disease of the arterial wall that leads to myocardial infarction and stroke. Regulatory T cells (Tregs) and IL‐10 exert significant anti‐atherogenic effects in experimental models of atherosclerosis by modulating vascular inflammation. We have previously shown that Mycobacterium bovis BCG killed by extended freeze‐drying (EFD BCG) decreases lung and colon inflammation by recruiting IL‐10‐producing Tregs. Therefore, the aim of this study was to investigate the effect of EFD BCG on the development of atherosclerosis.DesignWe used two strains of atherosclerosis‐prone mice: Ldlr−/− (four or six EFD BCG injections) and Apoe−/− (six injections).ResultsIn both models, EFD BCG significantly reduced the size of atherosclerotic lesions, increased IL‐10 production and reduced the serum levels of pro‐inflammatory cytokines (IL‐6, IL‐13, KC and tumour necrosis factor‐α). Shortly after treatment with EFD BCG, the number of plasmacytoid dendritic cells (pDCs) and Foxp3+ Tregs in the draining lymph nodes increased. EFD BCG also led to accumulation of Tregs, but not of pDCs in the spleen, and reduced activity of NF‐κB and increased activity of PPAR‐γ in both the spleen and vascular tissue of treated mice.ConclusionEFD BCG has atheroprotective effects through IL‐10 production and Treg expansion. These findings support a novel approach to the prevention and treatment of atherosclerosis.
Optimal Incentives with State‐Dependent Preferences
Authors: HWANG SUNG‐HA , BOWLES SAMUEL 
Published: August 2013

AbstractIn both experimental and natural settings, incentives sometimes underperform, generating smaller effects on the targeted behaviors than would be predicted for entirely self‐regarding agents. A parsimonious explanation is that incentives that appeal to self‐regarding economic motives may crowd out noneconomic motives such as altruism, reciprocity, intrinsic motivation, ethical values, and other social preferences, leading to disappointing and sometimes even counterproductive incentive effects. We present evidence from behavioral experiments that crowding may take two forms: categorical (the effect on preferences depends only on the presence or absence of the incentive) or marginal (the effect depends on the extent of the incentive). We extend an earlier contribution (Bowles and Hwang, ) to include categorical crowding, thus providing a more general framework for the study of optimal incentives and as a result, an expanded range of situations for which the sophisticated planner will (surprisingly) make greater use of incentives when incentives crowd out social preferences than when motivational crowding is absent.
Evaluation for effect of hypothermia on the disposition of 4-nitrophenol in rats by in-vitro metabolism study and rat liver perfusion system
Authors: Miyamoto Hirotaka , Matsueda Satoshi , Komori Kotaro , Fumoto Shintaro , Nakashima Mikiro , Yoshikawa Naoki , Hirata Haruna , Shimokawa Kenta , Ohwaki Yuichi , Nishida Koyo 
Published: August 2013

Abstract

Objectives
The aim of this study was to evaluate the effect of hypothermia on the in-vivo pharmacokinetics of 4-nitrophenol (4NP) using rat liver homogenate and rat liver perfusion system.

Methods
Rat liver homogenate was incubated with 4NP, which is mainly metabolized by cytochrome P450 2E1, at 37, 34, 32 or 28°C. The Michaelis constant (Km) and maximum elimination velocity (Vmax) of 4NP were calculated by a Hanes–Woolf plot. The hepatic extraction ratio (Eh) of 4NP was evaluated in a rat liver perfusion study at 37, 34, 32 or 28°C. Moreover, the plasma concentration profiles of 4NP after its intravenous (i.v.) administration to rats were analysed by the moment theory and were compared with in-vitro parameters.

Key findings
While the Km of 4NP was not changed, the Vmax and Eh were reduced at low temperatures. The plasma concentrations of 4NP after its i.v. administration to rats were significantly increased at 28°C.

Conclusion
Changes in the pharmacokinetics of 4NP under hypothermic conditions were caused by alterations in Vmax and Eh. We may be able to predict the disposition of a drug by in-vitro studies.
Substantial compositional turnover of fungal communities in an alpine ridge‐to‐snowbed gradient
Authors: Yao Fang , Vik Unni , Brysting Anne K. , Carlsen Tor , Halvorsen Rune , Kauserud Håvard 
Published: August 2013

AbstractThe main gradient in vascular plant, bryophyte and lichen species composition in alpine areas, structured by the topographic gradient from wind‐exposed ridges to snowbeds, has been extensively studied. Tolerance to environmental stress, resulting from wind abrasion and desiccation towards windswept ridges or reduced growing season due to prolonged snow cover towards snowbeds, is an important ecological mechanism in this gradient. The extent to which belowground fungal communities are structured by the same topographic gradient and the eventual mechanisms involved are less well known. In this study, we analysed variation in fungal diversity and community composition associated with roots of the ectomycorrhizal plant Bistorta vivipara along the ridge‐to‐snowbed gradient. We collected root samples from fifty B. vivipara plants in ten plots in an alpine area in central Norway. The fungal communities were analysed using 454 pyrosequencing analyses of tag‐encoded ITS1 amplicons. A distinct gradient in the fungal community composition was found that coincided with variation from ridge to snowbeds. This gradient was paralleled by change in soil content of carbon, nitrogen and phosphorus. A large proportion (66%) of the detected 801 nonsingleton operational taxonomic units (OTUs) were ascomycetes, while basidiomycetes dominated quantitatively (i.e. with respect to number of reads). Numerous fungal OTUs, many with taxonomic affinity to Sebacinales, Cortinarius and Meliniomyces, showed distinct affinities either to ridge or to snowbed plots, indicating habitat specialization. The compositional turnover of fungal communities along the gradient was not paralleled by a gradient in species richness.
Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera, Podarcis pityusensis (Squamata: Lacertidae)
Authors: Rodríguez V. , Brown R. P. , Terrasa B. , Pérez‐Mellado V. , Castro J. A. , Picornell A. , Ramon M. M. 
Published: August 2013

AbstractTwo monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time‐calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This suggests a mid‐late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089–0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present‐day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.
The Schizosaccharomyces pombe fusion gene hal3 encodes three distinct activities
Authors: Molero Cristina , Petrényi Katalin , González Asier , Carmona Mercè , Gelis Samuel , Abrie J. Albert , Strauss Erick , Ramos José , Dombradi Viktor , Hidalgo Elena , Ariño Joaquín 
Published: August 2013

SummarySaccharomyces cerevisiae Hal3 and Vhs3 are moonlighting proteins, forming an atypical heterotrimeric decarboxylase (PPCDC) required for CoA biosynthesis, and regulating cation homeostasis by inhibition of the Ppz1 phosphatase. The Schizosaccharomyces pombe ORF SPAC15E1.04 (renamed as Sp hal3) encodes a protein whose amino‐terminal half is similar to Sc Hal3 whereas its carboxyl‐terminal half is related to thymidylate synthase (TS). We show that Sp Hal3 and/or its N‐terminal domain retain the ability to bind to and modestly inhibit in vitro S. cerevisiae Ppz1 as well as its S. pombe homolog Pzh1, and also exhibit PPCDC activity in vitro and provide PPCDC function in vivo, indicating that Sp Hal3 is a monogenic PPCDC in fission yeast. Whereas the Sp Hal3 N‐terminal domain partially mimics Sc Hal3 functions, the entire protein and its carboxyl‐terminal domain rescue the S. cerevisiae cdc21 mutant, thus proving TS function. Additionally, we show that the 70 kDa Sp Hal3 protein is not proteolytically processed under diverse forms of stress and that, as predicted, Sp hal3 is an essential gene. Therefore, Sp hal3 represents a fusion event that joined three different functional activities in the same gene. The possible advantage derived from this surprising combination of essential proteins is discussed.
A new link between stress response and nucleolar function during pollen development in Arabidopsis mediated by AtREN1 protein
Authors: REŇÁK DAVID , GIBALOVÁ ANTÓNIA , ŠOLCOVÁ KATARZYNA , HONYS DAVID 
Published: August 2013

AbstractHeat shock transcription factors (Hsfs) are involved in multiple aspects of stress response and plant growth. However, their role during male gametophyte development is largely unknown, although the generative phase is the most sensitive and critical period in the plant life cycle. Based on a wide screen of T‐DNA mutant lines, we identified the atren1 mutation (restricted to nucleolus1) in early male gametophytic gene At1g77570, which has the closest homology to HSFA5 gene, the member of a heat shock transcription factor (HSF) gene family. The mutation causes multiple defects in male gametophyte development in both structure and function. Because the mutation disrupts an early acting (AtREN1) gene, these pollen phenotype abnormalities appear from bicellular pollen stage to pollen maturation. Moreover, the consequent progamic phase is compromised as well as documented by pollen germination defects and limited transmission via male gametophyte. In addition, atren1/− plants are defective in heat stress (HS) response and produce notably higher proportion of aberrant pollen grains. AtREN1 protein is targeted specifically to the nucleolus that, together with the increased size of the nucleolus in atren1 pollen, suggests that it is likely to be involved in ribosomal RNA biogenesis or other nucleolar functions.
The metabolic acclimation of Arabidopsis thaliana to arsenate is sensitized by the loss of mitochondrial LIPOAMIDE DEHYDROGENASE2, a key enzyme in oxidative metabolism
Authors: CHEN WEIHUA , TAYLOR NICOLAS L. , CHI YINGJUN , MILLAR A. HARVEY , LAMBERS HANS , FINNEGAN PATRICK M. 
Published: August 2013

AbstractMitochondrial lipoamide dehydrogenase is essential for the activity of four mitochondrial enzyme complexes central to oxidative metabolism. The reduction in protein amount and enzyme activity caused by disruption of mitochondrial LIPOAMIDE DEHYDROGENASE2 enhanced the arsenic sensitivity of Arabidopsis thaliana. Both arsenate and arsenite inhibited root elongation, decreased seedling size and increased anthocyanin production more profoundly in knockout mutants than in wild‐type seedlings. Arsenate also stimulated lateral root formation in the mutants. The activity of lipoamide dehydrogenase in isolated mitochondria was sensitive to arsenite, but not arsenate, indicating that arsenite could be the mediator of the observed phenotypes. Steady‐state metabolite abundances were only mildly affected by mutation of mitochondrial LIPOAMIDE DEHYDROGENASE2. In contrast, arsenate induced the remodelling of metabolite pools associated with oxidative metabolism in wild‐type seedlings, an effect that was enhanced in the mutant, especially around the enzyme complexes containing mitochondrial lipoamide dehydrogenase. These results indicate that mitochondrial lipoamide dehydrogenase is an important protein for determining the sensitivity of oxidative metabolism to arsenate in Arabidopsis.
An autoimmune disease refractory to immunosuppressive regimens: Celiac disease diagnosed long after liver transplantation
Authors: Ecevit Çiğdem , Karakoyun Miray , Ünal Fatih , Yüksekkaya Hasan A. , Doğanavşargil Başak , Yağcı Raşit V. , Aydoğdu Sema 
Published: August 2013

AbstractCD is defined as T‐lymphocyte‐mediated gluten sensitivity. Although CD is known to affect the small intestine, it is nonetheless a multisystem disorder. Liver involvement in CD may vary from isolated hypertransaminasemia to cirrhosis. Because CD is an inappropriate immune response to gluten proteins, strict gluten‐free diet is the principal therapy, along with management of liver dysfunction. In patients who fail to respond to a gluten‐free diet, immunosuppressive drugs may improve intestinal inflammatory activity in untreated CD. The present case report is of a 25‐yr‐old woman with diarrhea lasting several weeks. The patient had received a liver transplant 13 yr earlier, and presented with cryptogenic cirrhosis diagnosed as CD. This appears to be the first case of its kind in which a pediatric long‐term liver transplant patient presents with diarrhea eventually diagnosed as CD whose diet included gluten, and who was treated by an immunosuppressive drug regimen. Because of the normalization of CD‐related antibodies in the post‐transplantation period without gluten restriction, CD should be part of a list of diagnostic possibilities in liver transplant patients presenting with diarrhea of unknown etiology.
Maturation Environment and Impact on Subsequent Developmental Competence of Bovine Oocytes
Authors: Wrenzycki C , Stinshoff H 
Published: August 2013

ContentsIn vitro production (IVP) of bovine embryos has been improved immensely throughout the last decades. Nevertheless, embryos generated in vitro still differ from their in vivo‐produced counterparts. It is possible to achieve blastocyst rates of up to 70% if in vivo‐matured oocytes are used. In contrast, if oocytes are matured in vitro, blastocyst rates are only half that of those matured in vivo. This rather limited success may be attributed to the heterogeneous population of oocytes which are normally retrieved from follicles of 3–8 mm rather than from preovulatory follicles. In contrast to the in vivo‐ovulated oocyte, these oocytes lack development up to the preovulatory stage and are matured in vitro. Therefore, much effort has been devoted to the establishment of non‐invasive and non‐perturbing means for selecting the most competent oocytes, for example the extensiveness and compactness of the cumulus–corona investment and the granulation of the ooplasm. In vitro culture (IVC) conditions have been enhanced in the last few years, mainly by adjustment of media formulations, whereas the in vitro maturation (IVM) protocols stay invariable. Consequently, maintaining or mimicking the in vivo situation in vitro will aid to improve the quality and developmental competence of the resulting matured oocyte. The scope of this review is to give an overview of the current situation of in vitro maturation of mammalian oocytes with emphasis on the bovine species. Special attention has been paid to the in vivo situation in the follicle and how a better understanding of these intrafollicular factors will aid to improve the in vitro maturation conditions.
Ensemble segmentation for GBM brain tumors on MR images using confidence‐based averaging
Authors: Huo Jing , Okada Kazunori , van Rikxoort Eva M. , Kim Hyun J. , Alger Jeffry R. , Pope Whitney B. , Goldin Jonathan G. , Brown Matthew S. 
Published: August 2013

Purpose:Ensemble segmentation methods combine the segmentation results of individual methods into a final one, with the goal of achieving greater robustness and accuracy. The goal of this study was to develop an ensemble segmentation framework for glioblastoma multiforme tumors on single‐channel T1w postcontrast magnetic resonance images.Methods:Three base methods were evaluated in the framework: fuzzy connectedness, GrowCut, and voxel classification using support vector machine. A confidence map averaging (CMA) method was used as the ensemble rule.Results:The performance is evaluated on a comprehensive dataset of 46 cases including different tumor appearances. The accuracy of the segmentation result was evaluated using theF1‐measure between the semiautomated segmentation result and the ground truth.Conclusions:The results showed that the CMA ensemble result statistically approximates the best segmentation result of all the base methods for each case.