bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systematic review examining the effects of therapeutic radioactive iodine on ovarian function and future pregnancy in female thyroid cancer survivors
Authors: Sawka Anna M. , Lakra Deepak C. , Lea Jane , Alshehri Bandar , Tsang Richard W. , Brierley James D. , Straus Sharon , Thabane Lehana , Gafni Amiram , Ezzat Shereen , George Susan R. , Goldstein David P. 
Published: February 2008

SummaryBackground  For women with differentiated thyroid carcinoma (DTC), the effect of radioactive iodine (RAI) therapy on gonadal and reproductive function is an important consideration.Objective and methods  We systematically reviewed controlled studies examining the gonadal and reproductive effects of RAI therapy in women and adolescents surviving DTC. We searched nine electronic databases. All abstracts and papers were independently reviewed by two reviewers.Results  After reviewing 349 unique citations and 61 full‐text papers, 16 papers including data from 3023 women or adolescents with DTC were included. All studies were observational, with no long‐term randomized control trial data. The age at first RAI treatment varied from 8 to 50 years and the cumulative activities of RAI administered for treatment varied from 30 to 1099 mCi. Transient absence of menstrual periods occurred in 8–27% of women within the first year after RAI, particularly in older women. In addition, RAI‐treated women experienced menopause at a slightly younger age than women not treated with RAI. In the first year after RAI therapy, several studies reported increased rates of spontaneous and induced abortions. However, RAI treatment for DTC was generally not associated with a significantly increased risk of long‐term infertility, miscarriage, induced abortions, stillbirths, or offspring neonatal mortality or congenital defects.Conclusions  In female survivors of DTC, there is little observational evidence to suggest important adverse effects of RAI treatment on gonadal function, fertility or pregnancy outcomes beyond 12 months, with the exception of a possible slightly earlier age of menopause.
Plasma matrix metalloproteinase‐9 levels and blood pressure in short children born small for gestational age and effects of growth hormone treatment
Authors: Willemsen Ruben H. , Van Dijk Marije , De Kort Sandra W. K. , Van Toorenenbergen Albert W. , Hokken‐Koelega Anita C. S. 
Published: February 2008

SummaryContext  Short small‐for‐gestational‐age (SGA) children have an increased systolic blood pressure (BP) that decreases during long‐term GH treatment. The underlying mechanism is still unknown. Matrix metalloproteinases (MMPs) are zinc‐dependent endoproteinases that are involved in the remodelling of the extracellular matrix (ECM) and are thought to play a role in atherosclerosis. High MMP‐9 levels are found in hypertensive patients and predict cardiovascular mortality.Objectives  To investigate whether GH treatment affects plasma MMP‐9 levels in short SGA children and whether these are related to BP.Design  Case–control study.Intervention  GH treatment vs. no treatment during 36 months.Patients  Thirty‐eight short SGA children receiving GH treatment vs. 17 sex‐ and age‐matched untreated short SGA controls.Outcome measure  Plasma MMP‐9 levels and BP were measured at baseline, and after 6, 12 and 36 months of study.Results  MMP‐9 decreased significantly during 3 years of GH treatment but remained similar in untreated SGA controls. After 3 years of GH treatment, MMP‐9 levels were significantly lower in the GH group than in the untreated SGA controls. Systolic BP SDS significantly decreased in the GH group but remained unaltered in the untreated SGA controls. MMP‐9 levels did not correlate with systolic or diastolic BP.Conclusions  Plasma MMP‐9 levels and systolic BP SDS decreased to almost 50% of baseline values in the GH group but remained unchanged in untreated SGA controls. Our data indicate that GH has a positive effect on both MMP‐9 levels and systolic BP SDS.
Visions of a more precise soil biology
Authors: Andrén O. , Kirchmann H. , Kätterer T. , Magid J. , Paul E. A. , Coleman D. C. 
Published: February 2008

SummarySoils have often been viewed as a black box. Soil biology is difficult to study with the precision we would wish, due to the presence of considerable soil heterogeneity, a huge diversity of organisms, and a plethora of interacting processes taking place in a complex physical‐chemical environment. We have isolated a tiny fraction of the known organisms, and the possible interactions of soil parent materials, landscape, land use, depth and time with the biota mean that we are to some extent still fumbling in the dark. There have been great advances, but we argue that the pace of advance could be faster. To progress, science needs new theory and concepts but also acceptable methodologies. Coherent and generally accepted theoretical knowledge exists in many areas, but there is a shortage of valid and exact methods to test new and sometimes even old hypotheses. New methods add knowledge, but they also can add to the confusion if they are not tied to the existing knowledge base. We speculate on how to improve soil biology through improving the way we perform and interpret research. Can we deal with soil variability? Can we measure the critical variables with adequate precision to test our hypotheses? Can we avoid reinventing the wheel? Can we find a balance between the freedom to test new and maybe even controversial ideas and the control and direction of research required by society?
Unification of single‐configuration seismic imaging processes
Authors: Jaramillo H. , Albertin U. 
Published: February 2008

ABSTRACTIn this paper we derive an integral formula that encompasses all linear processes on seismic data. These include migration, demigration and residual migration, as well as data mapping procedures such as transformation to zero offset, inverse transformation to zero offset, residual transformation to zero offset and offset continuation. The derivation of the equation is different from all previous approaches to unification. Here we do not use a cascaded operation between two operators, but rather the superposition principle. In this regard, the derivation is not only more fundamental, but also simpler and more general. We study the kinematics and the dynamics of these processes and show that the signals can be reconstructed asymptotically either by finding the envelope of particular surfaces or by stacking energy along “adjoint” surfaces. For example, in the case of migration, the first set of surfaces are isochrons, while the “adjoint” surfaces are diffraction responses. In practice, the distinction between these two types of surfaces is equivalent to choosing the order of the computational loops with regard to the input and output seismic traces.
A frequency criterion for optimal node selection in smoothing with cubic splines
Authors: Schleicher Jörg , Biloti Ricardo 
Published: February 2008

ABSTRACTWhen smoothing a function with high‐frequency noise by means of optimal cubic splines, it is often not clear how to choose the number of nodes. The more nodes are used, the closer the smoothed function will follow the noisy one. In this work, we show that more nodes mean a better approximation of Fourier coefficients for higher frequencies. Thus, the number of nodes can be determined by specifying a frequency up to which all Fourier coefficients must be preserved and increasing the number of nodes until this criterion is met. A comparison of the corresponding smoothing results with those obtained by filtering using moving average and moving median filters of corresponding length and a low pass with corresponding high‐cut frequency shows that optimal cubic splines yield better results as they preserve not only the desired low‐frequency band but also important high‐frequency characteristics.
Laboratory estimates of normal and shear fracture compliance
Authors: Lubbe R. , Sothcott J. , Worthington M.H. , McCann C. 
Published: February 2008

ABSTRACTLaboratory estimates of the normal (Bn) and shear (Bt) compliance of artificial fractures in samples of Jurassic and Carboniferous limestone under wet and dry conditions are presented. The experiments were performed over a range of confining pressures (from 5 MPa up to 60 MPa), at ultrasonic frequencies in a Triaxial Hoek cell, using the pulse‐echo reflection technique. The results of this study confirm that the Bn/Bt ratio of a fracture is dependent on the fluid fill. A value of Bn/ Bt of less than 0.05 was obtained for our wet (honey saturated) sample which is consistent with the prediction that this ratio should be close to zero for fluid saturated fractures. Values of Bn/Bt for the dry sample are significantly higher and increase with confining pressure from 0.2 to 0.5. It is suggested that a Bn/Bt ratio of 0.5 is probably a more representative value to use in modelling studies of gas filled fractures than the common assumption that Bn ≈ Bt.
2D PP/PS‐stereotomography: Application to a real 2D‐OBC dataset
Authors: Alerini M. , Lambaré G. , Baina R. , Podvin P. , Le Bégat S. 
Published: February 2008

ABSTRACTIt has been shown on an ‘ideal’ synthetic dataset that PP/PS‐stereotomography can estimate an accurate velocity model without any pairing of PP‐ and PS‐events. The P‐wave velocity model is first estimated using PP data and then, fixing this velocity field, the S‐wave velocity is estimated using the PS data. This method needed to be evaluated further and we present here the first application of PP/PS‐stereotomography to a real dataset: the 2D East‐West Mahogany OBC line (Gulf of Mexico). We are here confronted with data which do not fit our working assumptions: coherent noise (due to an approximate separation of PP‐ and PS‐events and some remaining multiples), probably some anisotropy and 3D effects. With a careful selection of the stereotomographic picks, which allows one to decrease the effect of the picked coherent noise by the automatic picker, our application can demonstrate the relevance of our approach in the upper part of the profile, where anisotropy and 3D effects might be low. We can thus estimate, without any pairing of PP‐ and PS‐events, a velocity field which provides not only flat common image gathers, but also PP‐ and PS‐depth migrated images located at the same positions. For the deeper part of the profile, a significant shift in depth appears. In addition to possible anisotropy, 3D effects and a more complex velocity field (‘salt body’), this is due to the quality of the PZ‐ and X‐components profiles: The PZ‐component profile where the PP‐stereotomographic picking is performed, is polluted by conflicting converted or multiple events and the X‐component profile, where the PS‐stereotomographic picking is performed, is highly noisy. This study emphasizes the need to develop accurate selection criteria for the stereotomographic picks.
General morphological and biological features of neoplasms: integration of molecular findings
Authors: Diaz‐Cano S J 
Published: February 2008

This review highlights the importance of morphology–molecular correlations for a proper implementation of new markers. It covers both general aspects of tumorigenesis (which are normally omitted in papers analysing molecular pathways) and the general mechanisms for the acquired capabilities of neoplasms. The mechanisms are also supported by appropriate diagrams for each acquired capability that include overlooked features such as mobilization of cellular resources and changes in chromatin, transcription and epigenetics; fully accepted oncogenes and tumour suppressor genes are highlighted, while the pathways are also presented as activating or inactivating with appropriate colour coding. Finally, the concepts and mechanisms presented enable us to understand the basic requirements for the appropriate implementation of molecular tests in clinical practice. In summary, the basic findings are presented to serve as a bridge to clinical applications.The current definition of neoplasm is descriptive and difficult to apply routinely. Biologically, neoplasms develop through acquisition of capabilities that involve tumour cell aspects and modified microenvironment interactions, resulting in unrestricted growth due to a stepwise accumulation of cooperative genetic alterations that affect key molecular pathways. The correlation of these molecular aspects with morphological changes is essential for better understanding of essential concepts as early neoplasms/precancerous lesions, progression/dedifferentiation, and intratumour heterogeneity. The acquired capabilities include self‐maintained replication (cell cycle dysregulation), extended cell survival (cell cycle arrest, apoptosis dysregulation, and replicative lifespan), genetic instability (chromosomal and microsatellite), changes of chromatin, transcription and epigenetics, mobilization of cellular resources, and modified microenvironment interactions (tumour cells, stromal cells, extracellular, endothelium). The acquired capabilities defining neoplasms are the hallmarks of cancer, but they also comprise useful tools to improve diagnosis and prognosis, as well as potential therapeutic targets. The application of these concepts in oncological pathology leads to consideration of the molecular test requirements (Molecular Test Score System) for reliable implementation; these requirements should cover biological effects, molecular pathway, biological validation, and technical validation. Sensible application of molecular markers in tumour pathology always needs solid morphological support.
Dissection of spontaneous cytotoxicity by human intestinal intraepithelial lymphocytes: MIC on colon cancer triggers NKG2D‐mediated lysis through Fas ligand
Authors: Ebert Ellen C , Groh Veronika 
Published: February 2008

SummaryHuman intestinal intraepithelial lymphocytes (IELs), which are T‐cell receptor αβ+ CD8+ T cells located between epithelial cells (ECs), are likely to participate in the innate immune response against colon cancer. IELs demonstrate spontaneous cytotoxic (SC) activity specifically directed against EC tumours but not against other solid tumour types. The aim of this study was to dissect out the mechanism of SC activity, focusing on the interaction of NKG2D on IELs with its ligands [major histocompatibility complex (MHC) class I chain‐related protein (MIC) and UL16 binding protein (ULBP)] found mainly on EC tumours. A novel series of events occurred. The NKG2D–MIC/ULBP interaction induced Fas ligand (FasL) production and FasL‐mediated SC activity against HT‐29 cells and MIC‐transfectants. Tumour necrosis factor‐α and interferon‐γ, produced independently of this interaction, promoted SC activity. The immune synapse was strengthened by the interaction of CD103 on IELs with E‐cadherin on HT‐29 cells. Neither T‐cell receptor nor MHC class I was involved. While the HT‐29 cells were destroyed by soluble FasL, tumour necrosis factor‐α and interferon‐γ, the IELs were resistant to the effects of these mediators and to FasL expressed by the HT‐29 cells. This unidirectional FasL‐mediated cytotoxicity of IELs against HT‐29 cells, triggered through NKG2D, is unique and is likely to be a property of those CD8+ tumour‐infiltrating lymphocytes that phenotypically resemble IELs.
Rapid expansion of lichen woodlands within the closed‐crown boreal forest zone over the last 50 years caused by stand disturbances in eastern Canada
Authors: Girard F. , Payette S. , Gagnon R. 
Published: February 2008

AbstractAim  Our two main goals are first to evaluate the resilience of the boreal forest according to latitude across the closed‐crown forest zone using the post‐disturbance distribution and cover of lichen woodlands and closed‐crown forests as a metric, and second to identify the disturbance factors responsible for the regeneration and degradation of the closed‐crown forest according to latitude since the 1950s.Location  The study area extends between 70°00′ and 72°00′ W and throughout the closed‐crown forest zone, from its southern limit near 47°30′ N to its northern limit at the contact with the lichen woodland zone at around 52°40′ N.Methods  Recent (1972–2002) and old (1954–1956) aerial photos were used to map the distribution of lichen woodlands across the closed‐crown forest zone. Forest disturbances such as fire, spruce budworm (Choristoneura fumiferana (Clemens)) outbreak, and logging were recorded on each set of aerial photos. Each lichen woodland and stand disturbance was validated by air‐borne surveys and digitized using GIS software.Results  Over the last 50 years, the area occupied by lichen woodlands has increased according to latitude; that is, 9% of the area that was occupied by closed‐crown forests has shifted to lichen woodlands. Although logging activities have been concentrated in the same areas during the last 50 years, the area covered by logging has increased significantly. Outbreaks by the spruce budworm occurred predominantly in the southern (47°30′ N to 48°30′ N) and central (48°53′ N to 50°42′ N) parts of the study area, where balsam fir stands are extensive. In the northern part of the study area (51°–52°40′ N), extensive fires affected the distribution and cover of closed‐crown forests and lichen woodlands.Main conclusions  Over the last 50 years, the area occupied by closed‐crown forests has decreased dramatically, and the ecological conditions that allow closed‐crown forests to establish and develop are currently less prevalent. Fire is by far the main disturbance, reducing the ability of natural closed‐crown forests to self‐regenerate whatever the latitude. Given the current biogeographical shift from dense to open forests, the northern part of the closed‐crown forest zone is in a process of dramatic change towards the dominance of northern woodlands.
High tropical net diversification drives the New World latitudinal gradient in palm (Arecaceae) species richness
Authors: Svenning Jens‐Christian , Borchsenius Finn , Bjorholm Stine , Balslev Henrik 
Published: February 2008

AbstractAim Species richness exhibits striking geographical variation, but the processes that drive this variation are unresolved. We investigated the relative importance of two hypothesized evolutionary causes for the variation in palm species richness across the New World: time for diversification and evolutionary (net diversification) rate. Palms have a long history in the region, with the major clades diversifying during the Tertiary (65–2 Ma).Location Tropical and subtropical America (34° N–34° S; 33–120° W).Methods Using range maps, palm species richness was estimated in a 1° × 1° grid. Mean lineage net diversification was estimated by the mean phylogenetic root distance (MRD), the average number of nodes separating a species from the base of the palm phylogeny for the species in each grid cell. If evolutionary rate limits richness, then richness should increase with MRD. If time limits richness, then old, relict species (with low root distance) should predominantly occur in long‐inhabited and therefore species‐rich areas. Hence, richness should decrease with MRD. To determine the influence of net diversification across different time frames, MRD was computed for subtribe, genus and species levels within the phylogeny, and supplemented with the purely tip‐level measure, mean number of species per genus (MS/G). Correlations and regressions, in combination with eigenvector‐based spatial filtering, were used to assess the relationship between species richness, the net diversification measures, and potential environmental and geographical drivers.Results Species richness increased with all net diversification measures. The regression models showed that richness and the net diversification measures increased with decreasing (absolute) latitude and, less strongly, with increasing energy/temperature and water availability. These patterns therefore reflect net diversification at both deep and shallow levels in the phylogeny. Richness also increased with range in elevation, but this was only reflected in the MS/G pattern and therefore reflects recent diversification.Main conclusions The geographical patterns in palm species richness appear to be predominantly the result of elevated net diversification rates towards the equator and in warm, wet climates, sustained throughout most of the Tertiary. Late‐Tertiary orogeny has caused localized increases in net diversification rates that have also made a mark on the richness pattern.
Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans
Authors: BAÏLLE DOROTHÉE , BARRIÈRE ANTOINE , FÉLIX MARIE‐ANNE 
Published: February 2008

AbstractThe nematode Oscheius tipulae belongs to the same family (Rhabditidae) as the model species Caenorhabditis elegans. Both species reproduce through self‐fertilizing hermaphrodites and facultative males. Recent studies have shown that the self‐fertile C. elegans and C. briggsae displayed a 20‐fold lower genetic diversity than the male–female species C. remanei. Several explanations have been put forward to account for this difference, including their mode of reproduction and dynamic population structure. Here, we present the results of extensive worldwide sampling of O. tipulae, which we previously used as a laboratory organism for developmental genetics. We found that O. tipulae is much more widespread and common in soil throughout the world than Caenorhabditis species. We analysed 63 O. tipulae isolates from several continents using amplified fragment length polymorphism (AFLP). We found that O. tipulae harbours a 5‐fold higher genetic diversity than C. elegans and C. briggsae. As in C. elegans, a high proportion of this diversity was found locally. Yet, we detected significant geographical differentiation, both at the worldwide scale with a latitudinal structure and between three localities in France. In summary, O. tipulae exhibited significantly higher levels of genetic diversity and large‐scale geographical structure than C. elegans, despite their shared mode of reproduction. This species difference in genetic diversity may be explained by a number of other differences, such as population size, distribution, migration and dynamics. Due to its widespread occurrence and relatively high genetic diversity, O. tipulae may be a promising study species for evolutionary studies.
Sequencing goes 454 and takes large‐scale genomics into the wild
Authors: ELLEGREN HANS 
Published: February 2008

AbstractSometimes, science takes a big leap forward. This is often due to new technology that allows the study of questions previously difficult or even impossible to address. An example of this is provided in this issue (Veraet al. 2008) by the first large‐scale attempt toward genome sequencing of an ecologically important model, based on the new ‘454‐sequencing technology’. Using this new technology, the protein‐coding sequences of the Glanville fritillary butterfly genome have now been largely characterized.