bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dolomite formation in the shallow seas of the Alpine Triassic
Authors: Meister Patrick , Mckenzie Judith A. , Bernasconi Stefano M. , Brack Peter 
Published: October 2012

AbstractThe Alpine Triassic units of Switzerland, Northern Italy and Western Austria offer an extensive geological archive, in which the enigmatic process of dolomite formation can be studied in a palaeoenvironmental context. Recent studies clearly demonstrate that large amounts of the Alpine Triassic dolomites are late diagenetic or hydrothermal. Nevertheless, as part of multiple generations of diagenetic overprint, some generations of fine‐crystalline, Ca‐rich dolomite appear strictly confined to their depositional facies and show signs of very early formation at surface temperatures in specific ancient depositional environments. In this review, three cases of Alpine Triassic dolomites are discussed, where dolomite rocks may have formed during or soon after sedimentation. The sedimentary facies indicate contrasting palaeoenvironmental conditions and, hence, document three different possible processes of dolomite formation: (i) In the Dolomite Mountains (Northern Italy), dolomite beds of the partly isolated Middle Triassic (Anisian/Ladinian) Latemar Platform are confined to the very top of shallowing‐upward lagoonal facies cycles. (ii) Dolomite beds of the San Giorgio Basin (Southern Switzerland), an intra‐platform basin that opened during the Anisian/Ladinian transition, are associated with organic carbon‐rich shales, which were deposited in a deeper water environment under anoxic conditions. (iii) In the entirely dolomitized platform facies of the Dolomia Principale (Hauptdolomit Formation), a very early generation of fine‐crystalline dolomite occurs in the shallowest part of evaporative peritidal cycles. This platform extended over thousands of square kilometres along the Tethys margin during the Late Triassic (Carnian and Norian) and large amounts of carbonate were deposited under hypersaline sabkha‐like conditions. Representing three distinct depositional environments, these three different Triassic systems show features in common with several dolomitization models developed from the study of modern dolomite‐forming environments; for example, the sabkha model, the evaporative lagoon/lake model, the organogenic model and the microbial model. Although these actualistic models may be applicable to reconstruct the palaeoenvironmental conditions during dolomite formation, dolomite‐forming processes during the Triassic were apparently quite different from the modern world in terms of distribution and scale. Recent developments in stable‐isotope geochemistry and high‐resolution geochemical probing offer the possibility to make better reconstructions of Triassic palaeoceanographic conditions and suggest a non‐actualistic approach to better understand dolomite formation during the Triassic.
Beyond Welfare Regimes: From Empirical Typology to Conceptual Ideal types
Authors: Rice Deborah 
Published: October 2012

AbstractThe welfare regime concept introduced byGøstaEsping‐Andersen in 1990 is still widely used in comparative political research, although it has been challenged extensively both on empirical and analytical grounds. Besides the fact that many empirical welfare states seem to be hybrid cases of the established welfare regime categories, the argument that welfare regimes exist not only at the country level but also at the local level and at the level of particular welfare programmes has recently gained momentum in the academic literature. In this article, it is argued that the welfare regime concept should be stripped of its historical‐geographical connotations and turned into an ideal‐typical approach. To this end, a three‐dimensional model is proposed here that allows for analyzing the attributes of welfare states, welfare regions and welfare programmes on three analytical dimensions: welfare culture, welfare institutions and socio‐structural effects.
Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates, and cooperates with polynucleotide phosphorylase in 3′ end maturation
Authors: Germain Arnaud , Kim Sang Hu , Gutierrez Ryan , Stern David B. 
Published: October 2012

SummaryRibonuclease R (RNR1) and polynucleotide phosphorylase (cpPNPase) are the two known 3′→5′ exoribonucleases in Arabidopsis chloroplasts, and are involved in several aspects of rRNA and mRNA metabolism. In this work, we show that mutants lacking both RNR1 and cpPNPase exhibit embryo lethality, akin to the non‐viability of the analogous double mutant in Escherichia coli. We were successful, however, in combining an rnr1 null mutation with weak pnp mutant alleles, and show that the resulting chlorotic plants display a global reduction in RNA abundance. Such a counterintuitive outcome following the loss of RNA degradation activity suggests a major importance of RNA maturation as a determinant of RNA stability. Detailed analysis of the double mutant demonstrates that the enzymes catalyze a two‐step maturation of mRNA 3′ ends, with RNR1 polishing 3′ termini created by cpPNPase. The bulky quaternary structure of cpPNPase compared with RNR1 could explain this activity split between the two enzymes. In contrast to the double mutants, the rnr1 single mutant overaccumulates most mRNA species when compared with the wild type. The excess mRNAs in rnr1 are often present in non‐polysomal fractions, and half‐life measurements demonstrate a substantial increase in the stability of most mRNA species tested. Together, our data reveal the cooperative activity of two 3′→5′ exoribonucleases in chloroplast mRNA 3′ end maturation, and support the hypothesis that RNR1 plays a significant role in the destabilization of mRNAs unprotected by ribosomes.
Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana
Authors: Degenkolbe Thomas , Giavalisco Patrick , Zuther Ellen , Seiwert Bettina , Hincha Dirk K. , Willmitzer Lothar 
Published: October 2012

SummaryFreezing injury is a major factor limiting the geographical distribution of plant species and the growth and yield of crop plants. Plants from temperate climates are able to increase their freezing tolerance during exposure to low but non‐freezing temperatures in a process termed cold acclimation. Damage to cellular membranes is the major cause of freezing injury in plants, and membrane lipid composition is strongly modified during cold acclimation. Forward and reverse genetic approaches have been used to probe the role of specific lipid‐modifying enzymes in the freezing tolerance of plants. In the present paper we describe an alternative ecological genomics approach that relies on the natural genetic variation within a species. Arabidopsis thaliana has a wide geographical range throughout the Northern Hemisphere with significant natural variation in freezing tolerance that was used for a comparative analysis of the lipidomes of 15 Arabidopsis accessions using ultra‐performance liquid chromatography coupled to Fourier‐transform mass spectrometry, allowing the detection of 180 lipid species. After 14 days of cold acclimation at 4°C the plants from most accessions had accumulated massive amounts of storage lipids, with most of the changes in long‐chain unsaturated triacylglycerides, while the total amount of membrane lipids was only slightly changed. Nevertheless, major changes in the relative amounts of different membrane lipids were also evident. The relative abundance of several lipid species was highly correlated with the freezing tolerance of the accessions, allowing the identification of possible marker lipids for plant freezing tolerance.
A GAL4‐based targeted activation tagging system in Arabidopsis thaliana
Authors: Waki Takamitsu , Miyashima Shunsuke , Nakanishi Miyako , Ikeda Yoichi , Hashimoto Takashi , Nakajima Keiji 
Published: October 2012

SummaryActivation tagging is a powerful tool for discovering novel genes that are not easily identified by loss‐of‐function (lof) screening due to genetic redundancy or lethality. Although the current activation tagging system, which involves a viral enhancer sequence, has been used for a decade, alternative methods that allow organ‐ or tissue‐specific activation are required to identify genes whose strong activation leads to loss of fertility or viability. Here, we established a GAL4/UAS activation‐tagging system in Arabidopsis thaliana. Host plants that express a synthetic transcription activator GAL4:VP16 (GV) in an organ‐ or tissue‐specific manner were transformed with a T‐DNA harboring tandem copies of UAS, a GAL4‐binding sequence. Using a post‐embryonic and root‐specific GV‐expressing line as the host plant, we isolated several dominant mutants with abnormal root tissue patterns, designated as uas‐tagged root patterning (urp) mutants, and identified their causal genes. Notably, most URP genes encoded putative transcription factors, indicating that the GAL4/UAS activation tagging system effectively identifies genes with regulatory functions. lof phenotypes of most URP genes were either local patterning defects or visible only if homologous genes were disrupted simultaneously or independently. Systemic overexpression of some URP genes resulted in seedling lethality. These results indicate that GAL4/UAS activation tagging is a powerful method for identifying genes with biological functions that are not readily identified by conventional screening methods.
Critically separable rational maps in families
Authors: Petsche Clayton 
Published: October 2012

AbstractGiven a number field K, we consider families of critically separable rational maps of degree d over K possessing a certain fixed-point and multiplier structure. With suitable notions of isomorphism and good reduction between rational maps in these families, we prove a finiteness theorem which is analogous to Shafarevich’s theorem for elliptic curves. We also define the minimal critical discriminant, a global object which can be viewed as a measure of arithmetic complexity of a rational map. We formulate a conjectural bound on the minimal critical discriminant, which is analogous to Szpiro’s conjecture for elliptic curves, and we prove that a special case of our conjecture implies Szpiro’s conjecture in the semistable case.
Kontsevich’s noncommutative numerical motives
Authors: Marcolli Matilde , Tabuada Gonçalo 
Published: October 2012

AbstractIn this article we prove that Kontsevich’s category NCnum(k)F of noncommutative numerical motives is equivalent to the one constructed by the authors in [Marcolli and Tabuada, Noncommutative motives, numerical equivalence, and semisimplicity, Amer. J. Math., to appear, available at arXiv:1105.2950]. As a consequence, we conclude that NCnum(k)F is abelian semi-simple as conjectured by Kontsevich.
Imaging the healing murine myocardial infarct in vivo: ultrasound, magnetic resonance imaging and fluorescence molecular tomography
Authors: Gray Gillian A. , White Christopher I. , Thomson Adrian , Kozak Agnieszka , Moran Carmel , Jansen Maurits A. 
Published: October 2012

New Findings
What is the topic of this review?This short review examines how advanced imaging can be used to assess remodelling of the heart non‐invasively following myocardial infarction in murine experimental models.
What advances does it highlight?We review recent advances in the application of high‐resolution ultrasound, magnetic resonance imaging (MRI) and fluorescence molecular tomography (FMT), as well as positron emission tomography (PET) and single‐photon excitation computed tomography (SPECT) for assessment of processes involved in infarct healing, e.g. inflammation, as well as global structural and functional analysis.
Improved understanding of the processes involved in infarct healing is required for identification of novel therapeutic targets to limit infarct expansion and consequent long‐term ventricular remodelling after myocardial infarction. Infarct healing can be modelled effectively in murine models of coronary artery ligation. While imaging the murine heart is challenging due to its size and high rate of contraction, advances in preclinical imaging now permit accurate assessment of myocardial structure and function in vivo after myocardial infarction. Furthermore, rapid development of a range of molecular probes for use in a number of imaging modalities allows more detailed in vivo analysis of processes, including inflammation, fibrosis and angiogenesis. Here we consider the practical application of in vivo imaging by magnetic resonance imaging, ultrasound and fluorescence molecular tomography for assessment of infarct healing in the mouse.
Understanding the physiology of heart failure through cellular and in vivo models‐towards targeting of complex mechanisms
Authors: Lehnart Stephan E. 
Published: October 2012

New Findings
What is the topic of this review?Heart failure is a progressive disease syndrome that, in the early stages, involves subtle tissue and cellullar changes. This review highlights novel imaging techniques that allow quantitative investigation of the underlying pathophysiological mechanisms in vivo.
What advances does it highlight?High‐content voltage imaging of the left ventricle showed significant conduction slowing in the mdx mouse model of heart failure, corresponding to selective loss of Na+ channels and dystrophin in the lateral cardiac myocyte membrane. Super‐resolution STED imaging after myocardial infarction uncovered proliferative, differential remodelling of individual T‐tubules and network properties leading to intracellular Ca2+ release heterogeneity. These techniques reveal potential mechanisms of arrhythmia susceptibility, tissue degeneration and contractile dysfunction.
Heart failure (HF) is a complex disease syndrome, which affects physiology at all levels, from the molecule to the whole organism. Following a causative insult, a maladaptive response occurs, which sustains cardiac remodelling and leads to a final common pathway of debilitating HF symptoms. In terms of mechanisms, distinct defects of excitation–contraction coupling compartments and organelles have been identified in cardiac samples of patients and animal models, which include changes in Ca2+ transport proteins and T‐tubules. From a physiological standpoint, the source of regulatory intracellular Ca2+ is defined by ∼20,000 Ca2+ release units per cardiac myocyte, which jointly modulate contractile force production. We and others have characterized key changes in protein and membrane components of Ca2+ release units during HF in patient samples and transgenic models to gain insight into complex disease mechanisms. While earlier HF studies identified intracellular Ca2+ release as a major cause of contractile dysfunction, electrical dysfunction has gained attention as an important mechanism of HF mortality. In parallel, high‐resolution imaging techniques have become instrumental to understand HF mechanisms in the intact cell and tissue environment, supporting translation of novel diagnostic strategies. Indeed, the increased spatial and temporal resolution of different experimental imaging techniques addresses the vastly different scales of HF pathophysiology, to correlate experimental with clinical surrogate markers, and to extend mechanisms to early, often subtle changes in HF. This last goal, in particular, will be essential to translate novel pathophysiological insight back to the growing number of asymptomatic individuals at increased risk for HF development, who may benefit most from early therapeutic interventions.
The identification of genetic pathways involved in vascular adaptations after physical deconditioning versus exercise training in humans
Authors: Lammers Gerwen , van Duijnhoven Noortje T. L. , Hoenderop Joost G. , Horstman Astrid M. , de Haan Arnold , Janssen Thomas W. J. , de Graaf Mark J. J. , Pardoel Elisabeth M. , Verwiel Eugène T. P. , Thijssen Dick H. J. , Hopman Maria T. E. 
Published: October 2012

New Findings
What is the central question of this study?The aim of this study is to identify genes that are involved in vascular adaptations after physical deconditioning and exercise training in humans.
What is the main finding and its importance?Using unique human in vivo models for local deconditioning and exercise training, we demonstrate that the vascular endothelial growth factor signalling pathway, regulation through transforming growth factor β1 and extracellular matrix‐related genes are likely to be involved in vascular adaptations after physical (in)activity.
Physical inactivity and exercise training result in opposite adaptations of vascular structure. However, the molecular mechanisms behind these adaptations are not completely understood. We used a unique study design to examine both vascular characteristics of the superficial femoral artery (using ultrasound) and gene expression levels (from a muscle biopsy) in human models for physical deconditioning and exercise training. Initially, we compared able‐bodied control subjects (n = 6) with spinal cord‐injured individuals (n = 8) to assess the effects of long‐term deconditioning. Subsequently, able‐bodied control subjects underwent short‐term lower limb deconditioning using 3 weeks of unilateral limb suspension. Spinal cord‐injured individuals were examined before and after 6 weeks of functional electrical stimulation exercise training. Baseline femoral artery diameter and hyperaemic flow were lower after short‐ and long‐term deconditioning and higher after exercise training, whilst intima–media thickness/lumen ratio was increased with short‐ and long‐term deconditioning and decreased with exercise training. Regarding gene expression levels of vasculature‐related genes, we found that groups of genes including the vascular endothelial growth factor pathway, transforming growth factor β1 and extracellular matrix proteins were strongly associated with vascular adaptations in humans. This approach resulted in the identification of important genes that may be involved in vascular adaptations after physical deconditioning and exercise.
Dosimetric investigation of accelerated partial breast irradiation (APBI) using CyberKnife
Authors: Xu Qianyi , Chen Yan , Grimm Jimm , Fan Jiajin , An Lili , Xue Jinyu , Pahlajani Niraj , LaCouture Tamara 
Published: October 2012

Purpose:To investigate the dosimetric feasibility of accelerated partial breast irradiation (APBI) using CyberKnife.Methods:Fourteen previously treated patients with early‐stage breast cancer were selected for a retrospective study. Six of these patients had been treated to 38.5 Gy in 10 fractions in a phase III accelerated partial breast trial and the rest of the patients were treated to 50.4 Gy in 28 fractions. In this planning study, the guidelines in the protocol for the phase III partial breast trial were followed for organ delineation and CyberKnife planning. The achievable dosimetric parameters from all CyberKnife plans were compared to Intensity‐modulated radiation therapy (IMRT) and 3D‐CRT methods. The reproducibility of the dose delivery with and without respiratory motion was assessed through delivering a patient plan to a breast phantom. Different dose calculation algorithms were also compared between ray tracing and Monte Carlo.Results:For all the patients in the study, the dosimetric parameters met the guidelines from the NSABP B39/RTOG 0413 protocol strictly. The mean PTV volume covered by 100% of the prescription dose was 95.7 ± 0.7% (94.7%–97.1%). The mean maximal dose was 104 ± 2% of the prescription dose. The mean V50% and mean V100% to the ipsilateral normal breast were 23.1 ± 11.6% and 9.0 ± 5.8%, respectively. The conformity index of all plans was 1.14 ± 0.04. The maximum dose to the contralateral breast varied from 1.3 cGy to 111 cGy. The mean V5% and mean V30% to the contralateral and ipsilateral lungs were 1.0 ± 1.6% and 1.3 ± 1.2%, respectively. In our study, the mean V5% to the heart was 0.2 ± 0.5% for right‐sided tumors and 9.4 ± 10.1% for left‐sided tumors. Compared with IMRT and 3D‐CRT planning, the PTV coverage from CyberKnife planning was the highest, and the ratio of V20% to V100% of the breast from CyberKnife planning was the smallest. The heart and lung doses were similar in all the techniques except that the V5% for the lung and heart in CyberKnife planning was slightly higher.Conclusions:The dosimetric feasibility of APBI using CyberKnife was investigated in this retrospective study. All the dosimetric parameters strictly met the guidelines from the NSABP B39/RTOG 0413 protocol. With advanced real‐time tracking capability, CyberKnife should provide better target coverage and spare nearby critical organs for APBI treatment.
Dosimetric effect of intrafraction tumor motion in phase gated lung stereotactic body radiotherapy
Authors: Zhao Bo , Yang Yong , Li Tianfang , Li Xiang , Heron Dwight E. , Huq M. Saiful 
Published: October 2012

Purpose:A major concern for lung intensity modulated radiation therapy delivery is the deviation of actually delivered dose distribution from the planned one due to simultaneous movements of multileaf collimator (MLC) leaves and tumor. For gated lung stereotactic body radiotherapy treatment (SBRT), the situation becomes even more complicated because of SBRTˈs characteristics such as fewer fractions, smaller target volume, higher dose rate, and extended fractional treatment time. The purpose of this work is to investigate the dosimetric effect of intrafraction tumor motion during gated lung SBRT delivery by reconstructing the delivered dose distribution with real‐time tumor motion considered.Methods:The tumor motion data were retrieved from six lung patients. Each of them received three fractions of stereotactic radiotherapy treatments with Cyberknife Synchrony (Accuray, Sunnyvale, CA). Phase gating through an external surrogate was simulated with a gating window of 5 mm. The resulting residual tumor motion curves during gating (beam‐on) were retrieved. Planning target volume (PTV) was defined as physician‐contoured clinical target volume (CTV) surrounded by an isotropic 5 mm margin. Each patient was prescribed with 60 Gy/3 fractions. The authors developed an algorithm to reconstruct the delivered dose with tumor motion. The DMLC segments, mainly leaf position and segment weighting factor, were recalculated according to the probability density function of tumor motion curve. The new DMLC sequence file was imported back to treatment planning system to reconstruct the dose distribution.Results:Half of the patients in the study group experienced PTV D95% deviation up to 26% for fractional dose and 14% for total dose. CTV mean dose dropped by 1% with tumor motion. Although CTV is almost covered by prescribed dose with 5 mm margin, qualitative comparison on the dose distributions reveals that CTV is on the verge of underdose. The discrepancy happens due to tumor excursion outside of the gating window, which, for our study group, is mainly caused by baseline shift, i.e., the change in general trend of the motion curve during extended period of treatment time.Conclusions:The dose deviation in PTV and CTV due to target motion is not always negligible in gated SBRT. Although CTVs are covered sufficiently with prescribed dose in most cases, some are on the verge of underdose due to large tumor excursion caused by factors such as baseline shift.