bluuebunny/crossref_metadata_2025_split huggingface dataset:
Absence from work and emotional stress in women undergoing IVF or ICSI: An analysis of IVF‐related absence from work in women and the contribution of general and emotional factors
Authors: BOUWMANS CLAZIEN A.M. , LINTSEN BEA A.M.E. , AL MAIWEN , VERHAAK CHRIS M. , EIJKEMANS RENÉ J.C. , HABBEMA J. DIK F. , BRAAT DIDI D.M. , HAKKAART‐VAN ROIJEN LEONA 
Published: October 2008

AbstractObjective. To assess productivity losses due to absence from work during in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) treatment and to describe the pattern of IVF‐related absence from work. Additionally, the influence of general and psychological variables on IVF‐related absence from work was analyzed. Design. Prospective cohort study. Setting. Eight IVF hospitals participated in the study. Sample. Women undergoing their first treatment with IVF/ICSI. Methods. The Health and Labour Questionnaire (HLQ) was used to estimate the costs of IVF‐related absence from work (n = 384). Diaries were used to collect background information and reasons for IVF‐related absence. Psychological data were derived using the Spielberger State and Trait Anxiety Inventory (STAI), the Beck Depression Inventory for Primary Care (BDI‐PC) and the Inventory Social Relations and the Illness Cognition Questionnaire. Regression analyses were performed using two models, one without and one with psychological data, to assess the impact of the different variables on IVF‐related absence from work. Main outcome measure. IVF‐related absence from work and the costs of productivity losses due to IVF/ICSI per treatment. Results. Overall absence from work during IVF/ICSI treatment was on average 33 hours, of which 23 hours were attributed to IVF/ICSI. Costs of productivity losses due to IVF/ICSI were €596 per woman. Significant predictors of IVF‐related absence from work were the number of hours of paid work, age and self‐reported physical and/or emotional problems due to IFV treatment. Conclusions. Women experiencing emotional complaints and women with physical complaints due to IVF/ICSI reported significantly more IVF‐related absence from work.
Uterus transplantation in the rat: Model development, surgical learning and morphological evaluation of healing
Authors: WRANNING CAIZA A. , AKHI SHAMINA N. , KURLBERG GÖRAN , BRÄNNSTRÖM MATS 
Published: October 2008

AbstractObjective. Experimental uterus transplantation is a growing research field with the aim to develop a treatment for women with absolute uterus factor infertility. The potential risks of surgery and immunosuppressive treatment involved in uterus transplantation need to be identified and minimized in appropriate animal models before clinical trials commence. The aim of the present study was to develop and evaluate a model for uterus transplantation in the rat that can be reproduced and used in future studies concerning critical aspects of uterine function after transplantation. Design. Animal study. Setting. University Hospital. Sample. Uterine tissue sampled at different post‐operative time points after non‐rejecting uterus transplantation in rats. Methods. Adult, virgin female rats of inbred Lewis strain served as donors and recipients of uterine transplants. Two individuals with no previous microsurgical training performed the transplantations and learning curves were recorded. When transplant survival exceeded 70% for both surgeons, 15 animals were transplanted and grafted uteri were evaluated at 1, 7 and 21 days after surgery by assessment of morphology and enumeration of infiltrating neutrophilic granulocytes. Main outcome measures. Animal survival, graft survival, surgery times, uterine morphology, enumeration of infiltrating neutrophilic granulocytes. Results. Both surgeons gained the necessary microsurgical skills needed to achieve above 70% transplant survival at a similar rate. The signs of post‐operative inflammation on day one after transplantation were minor and further reduced at later time points. Conclusion. A reproducible model for uterus transplantation in the rat was developed, which can be used in future studies concerning uterine function after allogenic transplantation.
Critical roles of VEGF‐C‐VEGF receptor 3 in reconnection of the collecting lymph vessels in mice
Authors: IKOMI FUMITAKA , KAWAI YOSHIKO , NAKAYAMA JUN , OGIWARA NAOKO , SASAKI KATSUNORI , MIZUNO RISUKE , OHHASHI TOSHIO 
Published: October 2008

ABSTRACTMolecular mechanisms of reconnection of collecting lymph vessels were analyzed by using murine popliteal prenodal lymph vessels. At 1 and 2 weeks after being divided by cutting the lymph vessel, lymphatic reconnection was frequently observed accompanied by mesh‐like lymphatic channels. Electron microscopic study also showed a monolayer of endothelial cells in the newly developed lymph vessels. Smooth muscle markers were immunofluorescently demonstrated in the wall of the new vessels. At 1 week after the procedure of cutting, augmented expressions of VEGF receptors 1, 2 and 3 were found immunohistochemically at the site of the reconnected lymph vessels. The expression of mRNA for VEGF receptor 3 was enhanced at 5 days and 1 week in small pieces of the tissues containing the reconnected lymph vessels, compared with that in the corresponding tissues obtained with sham operated ones. The administration of VEGF‐C at the cutting site of the collecting lymph vessel significantly increased the rate of the reconnected lymph vessels, whereas additional treatment with Flt4/Fc chimera protein significantly reduced the rate of the reconnected ones. These results suggest that activation of VEGF‐C‐VEGF receptor 3 has critical roles in reconnection of the collecting lymph vessels in adult mice.
Aggressive assembly of pyrosequencing reads with mates
Authors: Miller Jason R. , Delcher Arthur L. , Koren Sergey , Venter Eli , Walenz Brian P. , Brownley Anushka , Johnson Justin , Li Kelvin , Mobarry Clark , Sutton Granger 
Published: October 2008

Abstract
Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a ‘hybrid’ approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data.
Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data.
Availability: The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License.
Contact: jmiller@jcvi.org
Supplementary information: Supplementary data are available at Bioinformatics online.
MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics
Authors: Hundertmark C. , Fischer R. , Reinl T. , May S. , Klawonn F. , Jänsch L. 
Published: October 2008

Abstract
Motivation: Mass spectrometry (MS) data are impaired by noise similar to many other analytical methods. Therefore, proteomics requires statistical approaches to determine the reliability of regulatory information if protein quantification is based on ion intensities observed in MS.
Results: We suggest a procedure to model instrument and workflow-specific noise behaviour of iTRAQ™ reporter ions that can provide regulatory information during automated peptide sequencing by LC-MS/MS. The established mathematical model representatively predicts possible variations of iTRAQ™ reporter ions in an MS data-dependent manner. The model can be utilized to calculate the robustness of regulatory information systematically at the peptide level in so-called bottom-up proteome approaches. It allows to determine the best fitting regulation factor and in addition to calculate the probability of alternative regulations. The result can be visualized as likelihood curves summarizing both the quantity and quality of regulatory information. Likelihood curves basically can be calculated from all peptides belonging to different regions of proteins if they are detected in LC-MS/MS experiments. Therefore, this approach renders excellent opportunities to detect and statistically validate dynamic post-translational modifications usually affecting only particular regions of the whole protein. The detection of known phosphorylation events at protein kinases served as a first proof of concept in this study and underscores the potential for noise models in quantitative proteomics.
Contact: lothar.jaensch@helmholtz-hzi.de; f.klawonn@fh-wolfenbuettel.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Horse mackerel (Trachurus trachurus) stomach fullness off Portugal: index calibration and spatio-temporal variations in feeding intensity
Authors: Garrido Susana , Murta Alberto G. , Moreira Ana , Ferreira Maria João , Angélico Maria Manuel 
Published: October 2008

Abstract
Garrido, S., Murta, A. G., Moreira, A., Ferreira, M. J., and Angélico, M. M. 2008. Horse mackerel (Trachurus trachurus) stomach fullness off Portugal: index calibration and spatio-temporal variations in feeding intensity. – ICES Journal of Marine Science, 65: 1662–1669. An index for stomach fullness used in the routine biological sampling of horse mackerel from Portuguese waters was calibrated about the correspondent stomach mass. The fullness scale comprises four levels (1, empty; 2, <50% filled; 3, >50% filled; 4, bursting) that are easily attributed to whole stomachs during the sampling process. Significant differences were found among the four levels of the fullness scale in their relative stomach masses, indicating that the index can be used for the semi-quantitative analysis of feeding intensity in this species. The fullness index was applied to study spatio-temporal variations in horse mackerel feeding off the Portuguese coast, using data collected from 1985 to 2006 on commercial vessels and research cruises. There was no significant difference in feeding intensity between sexes. Smaller horse mackerel and those in the resting stage of reproduction fed more intensively than larger and spawning fish. Feeding intensities of fish from the southern and northwest coasts of Portugal were greater than for those captured along the southwest coast. Horse mackerel feeding intensity was greater at dawn and varied seasonally, being higher during spring and autumn and lower during winter. Interannual variation in feeding intensity of horse mackerel captured along the west coast of Portugal revealed a significant but slight decrease in recent years.
Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids
Authors: Lyons Eric , Pedersen Brent , Kane Josh , Alam Maqsudul , Ming Ray , Tang Haibao , Wang Xiyin , Bowers John , Paterson Andrew , Lisch Damon , Freeling Michael 
Published: October 2008

AbstractIn addition to the genomes of Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa), two near-complete rosid genome sequences, grape (Vitis vinifera) and papaya (Carica papaya), have been recently released. The phylogenetic relationship among these four genomes and the placement of their three independent, fractionated tetraploidies sum to a powerful comparative genomic system. CoGe, a platform of multiple whole or near-complete genome sequences, provides an integrative Web-based system to find and align syntenic chromosomal regions and visualize the output in an intuitive and interactive manner. CoGe has been customized to specifically support comparisons among the rosids. Crucial facts and definitions are presented to clearly describe the sorts of biological questions that might be answered in part using CoGe, including patterns of DNA conservation, accuracy of annotation, transposability of individual genes, subfunctionalization and/or fractionation of syntenic gene sets, and conserved noncoding sequence content. This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically.
Transforming a Fructan:Fructan 6G-Fructosyltransferase from Perennial Ryegrass into a Sucrose:Sucrose 1-Fructosyltransferase
Authors: Lasseur Bertrand , Schroeven Lindsey , Lammens Willem , Le Roy Katrien , Spangenberg German , Manduzio Hélène , Vergauwen Rudy , Lothier Jérémy , Prud'homme Marie-Pascale , Van den Ende Wim 
Published: October 2008

AbstractFructosyltransferases (FTs) synthesize fructans, fructose polymers accumulating in economically important cool-season grasses and cereals. FTs might be crucial for plant survival under stress conditions in species in which fructans represent the major form of reserve carbohydrate, such as perennial ryegrass (Lolium perenne). Two FT types can be distinguished: those using sucrose (S-type enzymes: sucrose:sucrose 1-fructosyltransferase [1-SST], sucrose:fructan 6-fructosyltransferase) and those using fructans (F-type enzymes: fructan:fructan 1-fructosyltransferase [1-FFT], fructan:fructan 6G-fructosyltransferase [6G-FFT]) as preferential donor substrate. Here, we report, to our knowledge for the first time, the transformation of an F-type enzyme (6G-FFT/1-FFT) into an S-type enzyme (1-SST) using perennial ryegrass 6G-FFT/1-FFT (Lp6G-FFT/1-FFT) and 1-SST (Lp1-SST) as model enzymes. This transformation was accomplished by mutating three amino acids (N340D, W343R, and S415N) in the vicinity of the active site of Lp6G-FFT/1-FFT. In addition, effects of each amino acid mutation alone or in combination have been studied. Our results strongly suggest that the amino acid at position 343 (tryptophan or arginine) can greatly determine the donor substrate characteristics by influencing the position of the amino acid at position 340. Moreover, the presence of arginine-343 negatively affects the formation of neofructan-type linkages. The results are compared with recent findings on donor substrate selectivity within the group of plant cell wall invertases and fructan exohydrolases. Taken together, these insights contribute to our knowledge of structure/function relationships within plant family 32 glycosyl hydrolases and open the way to the production of tailor-made fructans on a larger scale.
Replication of Nonautonomous Retroelements in Soybean Appears to Be Both Recent and Common
Authors: Wawrzynski Adam , Ashfield Tom , Chen Nicolas W.G. , Mammadov Jafar , Nguyen Ashley , Podicheti Ram , Cannon Steven B. , Thareau Vincent , Ameline-Torregrosa Carine , Cannon Ethalinda , Chacko Ben , Couloux Arnaud , Dalwani Anita , Denny Roxanne , Deshpande Shweta , Egan Ashley N. , Glover Natasha , Howell Stacy , Ilut Dan , Lai Hongshing , del Campo Sara Martin , Metcalf Michelle , O'Bleness Majesta , Pfeil Bernard E. , Ratnaparkhe Milind B. , Samain Sylvie , Sanders Iryna , Ségurens Béatrice , Sévignac Mireille , Sherman-Broyles Sue , Tucker Dominic M. , Yi Jing , Doyle Jeff J. , Geffroy Valérie , Roe Bruce A. , Maroof M.A. Saghai , Young Nevin D. , Innes Roger W. 
Published: October 2008

Abstract
Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.
RETARDED PALEA1 Controls Palea Development and Floral Zygomorphy in Rice
Authors: Yuan Zheng , Gao Shan , Xue Da-Wei , Luo Da , Li Lan-Tian , Ding Shu-Yan , Yao Xuan , Wilson Zoe A. , Qian Qian , Zhang Da-Bing 
Published: October 2008

Abstract
Poaceae, one of the largest flowering plant families in angiosperms, evolved distinct inflorescence and flower morphology diverging from eudicots and other monocots. However, the mechanism underlying the specification of flower morphology in grasses remains unclear. Here we show that floral zygomorphy along the lemma-palea axis in rice (Oryza sativa) is partially or indirectly determined by the CYCLOIDEA (CYC)-like homolog RETARDED PALEA1 (REP1), which regulates palea identity and development. The REP1 gene is only expressed in palea primordium during early flower development, but during later floral stages is radially dispersed in stamens and the vascular bundles of the lemma and palea. The development of palea is significantly retarded in the rep1 mutant and its palea has five vascular bundles, which is similar to the vascular pattern of the wild-type lemma. Furthermore, ectopic expression of REP1 caused the asymmetrical overdifferentiation of the palea cells, altering their floral asymmetry. This work therefore extends the function of the TCP gene family members in defining the diversification of floral morphology in grasses and suggests that a common conserved mechanism controlling floral zygomorphy by CYC-like genes exists in both eudicots and the grasses.
Root System Architecture inArabidopsisGrown in Culture Is Regulated by Sucrose Uptake in the Aerial Tissues
Authors: MacGregor Dana R. , Deak Karen I. , Ingram Paul A. , Malamy Jocelyn E. 
Published: October 2008

AbstractThis article presents a detailed model for the regulation of lateral root formation in Arabidopsis thaliana seedlings grown in culture. We demonstrate that direct contact between the aerial tissues and sucrose in the growth media is necessary and sufficient to promote emergence of lateral root primordia from the parent root. Mild osmotic stress is perceived by the root, which then sends an abscisic acid–dependent signal that causes a decrease in the permeability of aerial tissues; this reduces uptake of sucrose from the culture media, which leads to a repression of lateral root formation. Osmotic repression of lateral root formation in culture can be overcome by mutations that cause the cuticle of a plant's aerial tissues to become more permeable. Indeed, we report here that the previously described lateral root development2 mutant overcomes osmotic repression of lateral root formation because of a point mutation in Long Chain Acyl-CoA Synthetase2, a gene essential for cutin biosynthesis. Together, our findings (1) impact the interpretation of experiments that use Arabidopsis grown in culture to study root system architecture; (2) identify sucrose as an unexpected regulator of lateral root formation; (3) demonstrate mechanisms by which roots communicate information to aerial tissues and receive information in turn; and (4) provide insights into the regulatory pathways that allow plants to be developmentally plastic while preserving the essential balance between aboveground and belowground organs.
NIP6;1 Is a Boric Acid Channel for Preferential Transport of Boron to Growing Shoot Tissues inArabidopsis
Authors: Tanaka Mayuki , Wallace Ian S. , Takano Junpei , Roberts Daniel M. , Fujiwara Toru 
Published: October 2008

AbstractBoron (B) in soil is taken up by roots through NIP5;1, a boric acid channel, and is loaded into the xylem by BOR1, a borate exporter. Here, the function of Arabidopsis thaliana NIP6;1, the most similar gene to NIP5;1, was studied. NIP6;1 facilitates the rapid permeation of boric acid across the membrane but is completely impermeable to water. NIP6;1 transcript accumulation is elevated in response to B deprivation in shoots but not in roots. NIP6;1 promoter–β-glucuronidase is predominantly expressed in nodal regions of shoots, especially the phloem region of vascular tissues. Three independently identified T-DNA insertion lines for the NIP6;1 gene exhibited reduced expansion of young rosette leaves only under low-B conditions. B concentrations are reduced in young rosette leaves but not in the old leaves of these mutants. Taken together, these data strongly suggest that NIP6;1 is a boric acid channel required for proper distribution of boric acid, particularly among young developing shoot tissues. We propose that NIP6;1 is involved in xylem–phloem transfer of boric acid at the nodal regions and that the water-tight property of NIP6;1 is important for this function. It is proposed that during evolution, NIP5;1 and NIP6;1 were diversified in terms of both the specificity of their expression in plant tissues and their water permeation properties, while maintaining their ability to be induced under low B and their boric acid transport activities.
Conditional Repression of AUXIN BINDING PROTEIN1 Reveals That It Coordinates Cell Division and Cell Expansion during Postembryonic Shoot Development inArabidopsisand Tobacco
Authors: Braun Nils , Wyrzykowska Joanna , Muller Philippe , David Karine , Couch Daniel , Perrot-Rechenmann Catherine , Fleming Andrew J. 
Published: October 2008

AbstractAUXIN BINDING PROTEIN1 (ABP1) has long been characterized as a potentially important mediator of auxin action in plants. Analysis of the functional requirement for ABP1 during development was hampered because of embryo lethality of the null mutant in Arabidopsis thaliana. Here, we used conditional repression of ABP1 to investigate its function during vegetative shoot development. Using an inducible cellular immunization approach and an inducible antisense construct, we showed that decreased ABP1 activity leads to a severe retardation of leaf growth involving an alteration in cell division frequency, an altered pattern of endocycle induction, a decrease in cell expansion, and a change in expression of early auxin responsive genes. In addition, local repression of ABP1 activity in the shoot apical meristem revealed an additional role for ABP1 in cell plate formation and cell shape. Moreover, cells at the site of presumptive leaf initiation were more sensitive to ABP1 repression than other regions of the meristem. This spatial context-dependent response of the meristem to ABP1 inactivation and the other data presented here are consistent with a model in which ABP1 acts as a coordinator of cell division and expansion, with local auxin levels influencing ABP1 effectiveness.