bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of the success of phylogenetic inference in simulations
Authors: Simmons Mark P. , Webb Colleen T. 
Published: September 2010

AbstractFor phylogenetic simulation studies, the accuracy of topological reconstruction obtained from different data matrices or different methods of phylogenetic inference generally needs to be quantified. Two components of performance within this context are: (1) how the inferred tree topology matches or conflicts with the correct tree topology, and (2) the branch support assigned to both correctly and incorrectly resolved clades. We present a method (averaged overall success of resolution) that incorporates both of these components. Branch support is incorporated in the averaged overall success of resolution by linearly scaling the observed support relative to that conferred by uncontradicted synapomorphies. We believe that this method represents an improvement relative to the commonly used approaches of quantifying the percentage of clades that are correctly resolved in the inferred trees or presenting the Robinson–Foulds distance between the inferred trees and the correct tree. In contrast to Bremer support, the averaged overall success of resolution may be applied equally well to distance, likelihood and parsimony analyses.© The Willi Hennig Society 2006.
Development of invasive follicular cell carcinomas in a rat thyroid carcinogenesis model: Biological impact of capsular inflammation and reduced cyclooxygenase‐2 expression
Authors: Imai Toshio , Hasumura Mai , Onose Jun‐ichi , Ueda Makoto , Takizawa Tamotsu , Cho Young‐Man , Hirose Masao 
Published: September 2010

We have previously reported that thyroid capsular inflammation induced by sulfadimethoxine (SDM), a goitrogen, might play a role in development of invasive follicular cell adenocarcinomas in rats initiated with N‐bis(2‐hydroxypropyl)nitrosamine (DHPN). The present study was designed to examine the role of cyclooxygenase (COX)‐2, widely known to be up‐regulated in inflammatory states, during chemically induced rat thyroid carcinogenesis. Male F344 rats received a subcutaneous DHPN (2800 mg/kg) injection, and 1 week later were allowed free access to drinking water containing antithyroidal propylthiouracil (PTU, 0.003%) or SDM (0.1%) for 4 or 10 weeks. Control groups receiving goitrogen alone and no treatment were also included. At week 4, diffuse follicular cell hyperplasia was induced in all PTU‐ and SDM‐treated groups, along with fibrous capsular thickening and capsular thickening with inflammation, respectively. Additionally, multiple focal follicular cell hyperplasias and adenomas were observed in the DHPN + PTU and DHPN + SDM cases. At week 10, adenocarcinomas invasive to the capsule and restricted to the capsular adjacent region, were frequent in the DHPN + SDM group, but not observed in the animals given DHPN + PTU. Western blots and immunohistochemistry revealed constitutive COX‐2 expression in non‐neoplastic follicular cells of the control and all of the PTU‐ and SDM‐treated rats. However, COX‐2 reactivity was significantly reduced or negative in the preneoplastic/neoplastic lesions in the DHPN‐treated groups. In fibrous or inflamed thickened capsules, only a few component cells with inflammatory elements were positive for COX‐2, and there was no significant difference in this regard between the PTU and SDM treatments. The present results suggest that capsular inflammation could play a role in development of invasive carcinomas, but COX‐2 expression does not make a major contribution. (Cancer Sci 2005; 96: 31–38)
Possible enhancing effects of atrazine on growth of 7,12‐dimethylbenz(a) anthracene‐induced mammary tumors in ovariectomized Sprague–Dawley rats
Authors: Ueda Makoto , Imai Toshio , Takizawa Tamotsu , Onodera Hiroshi , Mitsumori Kunitoshi , Matsui Takane , Hirose Masao 
Published: September 2010

Atrazine, one of the most commonly used herbicides in the world, has been reported to have endocrine disrupting effects in vivo. In the present experiment, influence of dietary atrazine on the late promotion/progression stage of mammary carcinogenesis in ovariectomized female Sprague–Dawley rats was examined after a single intragastric administration of 7,12‐dimethylbenz(a)anthracene (DMBA). When the incidence of palpable mammary tumors reached about 50%, the animals were subjected to ovariectomy and divided into tumor bearing [DMBA‐Tumor(+)] and non‐tumor bearing [DMBA‐Tumor(–)] groups, with subgroups of each fed a soybean‐free diet containing 0, 5, 50, or 500 p.p.m. atrazine for 34 weeks. At the completion of the study, the tumor volume in the 50 and 500 p.p.m. treatment Tumor(+) subgroups was greater than in the 0 p.p.m. control case. In the DMBA‐Tumor(–) group, higher incidences and volumes of the mammary tumors, with or without statistical significance (P < 0.05), were observed in the 50 and 500 p.p.m. subgroups. Atrazine treatment tended to increase proportion of estrogen receptor α‐positive tumors and stimulated cell proliferation in the DMBA‐Tumor(+) group, but with no clear effects on serum hormone levels. The present study indicates that atrazine has a potential for enhancing the growth of mammary tumors, partly through increasing cell proliferation in the promotion/progression stage in female rats under ovarian hormone‐free conditions. (Cancer Sci 2005; 96: 19 –25)
Impact of menstrual and reproductive factors on breast cancer risk in Japan: Results of the JACC study
Authors: Tamakoshi Koji , Yatsuya Hiroshi , Wakai Kenji , Suzuki Sadao , Nishio Kazuko , Lin Yingsong , Niwa Yoshimitsu , Kondo Takaaki , Yamamoto Akio , Tokudome Shinkan , Toyoshima Hideaki , Tamakoshi Akiko ,   for the JACC Study Group
Published: September 2010

The incidence of breast cancer among Japanese women, a traditionally low‐risk population, has increased substantially. To evaluate the association of reproductive factors with breast cancer risk, we examined 38 159 Japanese women, aged 40–79 years, who responded to a questionnaire on reproductive and other lifestyle factors from 1988 to 1990 in the Japan Collaborative Cohort Study. During an average 7.6 years of follow‐up, we documented 151 incidents of breast cancers. Cox proportional hazards modeling was employed to estimate relative risks (RR) and 95% confidence intervals (CI). There was a significant decline in the risk of breast cancer with increasing parity among parous women (trend P = 0.01). Women with four or more parities had a 69% lower risk than uniparous women, a reduced risk was also evident among menopausal women. Breast cancer risk tended to rise with increasing age at first delivery (trend P = 0.05), the association being very apparent among menopausal women (trend P = 0.02). Compared to the women who had their first delivery before age 25, those who delayed this event until after age 34 had an RR of 2.12 (95% CI: 0.72–6.21) and 3.33 (1.07–10.3) among the overall subjects and the menopausal, respectively. There was no apparent association of breast cancer risk with age at menarche or menopause. Our study concerning reproductive risk factors suggests that breast cancer in Japan is similar to that in Western countries, and that reproductive factors, particularly the number of parity and age at first delivery, might be important in the etiology of breast cancer among Japanese women. (Cancer Sci 2005; 96: 57–63)
Inhibition of peroxisome proliferator‐activated receptor γ activity suppresses pancreatic cancer cell motility
Authors: Nakajima Atsushi , Tomimoto Ayako , Fujita Koji , Sugiyama Michiko , Takahashi Hirokazu , Ikeda Ikuko , Hosono Kunihiro , Endo Hiroki , Yoneda Kyoko , Iida Hiroshi , Inamori Masahiko , Kubota Kensuke , Saito Satoru , Nakajima Noriko , Wada Koichiro , Nagashima Yoji , Nakagama Hitoshi 
Published: September 2010

Peroxisome proliferator‐activated receptor γ (PPARγ) is a ligand‐activated transcription factor that has been implicated in the carcinogenesis and progression of various solid tumors, including pancreatic carcinomas. We aimed to clarify the role of this receptor in pancreatic cell motility in vitro and in metastasis in vivo. Cell motility was examined by assaying transwell migration and wound filling in Capan‐1 and Panc‐1 pancreatic cancer cells, with or without the PPARγ‐specific inhibitor T0070907. A severe combined immunodeficiency xenograft metastasis model was used to examine the in vivo effect of PPARγ inhibition on pancreatic cancer metastasis. In both transwell‐migration and wound‐filling assays, inhibition of PPARγ activity suppressed pancreatic cell motility without affecting in vitro cell proliferation. Inhibition of PPARγ also suppressed liver metastasis in vivo in metastatic mice. In PPARγ‐inhibited cells, p120 catenin accumulation was induced predominantly in cell membranes, and the Ras‐homologous GTPases Rac1 and Cdc42 were inactive. Inhibition of PPARγ in pancreatic cancer cells decreased cell motility by altering p120ctn localization and by suppressing the activity of the Ras‐homologous GTPases Rac1 and Cdc42. Based on these findings, PPARγ could function as a novel target for the therapeutic control of cancer cell invasion or metastasis. (Cancer Sci 2008; 99: 1892–1900)
Cross‐sectional analysis of germline BRCA1 and BRCA2 mutations in Japanese patients suspected to have hereditary breast/ovarian cancer
Authors: Sugano Kokichi , Nakamura Seigo , Ando Jiro , Takayama Shin , Kamata Hiroyuki , Sekiguchi Isao , Ubukata Megumi , Kodama Tetsuro , Arai Masami , Kasumi Fujio , Hirai Yasuo , Ikeda Tadashi , Jinno Hiromitsu , Kitajima Masaki , Aoki Daisuke , Hirasawa Akira , Takeda Yuko , Yazaki Kumiko , Fukutomi Takashi , Kinoshita Takayuki , Tsunematsu Ryuichiro , Yoshida Teruhiko , Izumi Masako , Umezawa Shino , Yagata Hiroshi , Komatsu Hiroko , Arimori Naoko , Matoba Noriko , Gondo Nobuhisa , Yokoyama Shiro , Miki Yoshio 
Published: September 2010

The prevalence of BRCA1/2 germline mutations in Japanese patients suspected to have hereditary breast/ovarian cancer was examined by a multi‐institutional study, aiming at the clinical application of total sequencing analysis and validation of assay sensitivity in Japanese people using a cross‐sectional approach based on genetic factors estimated from personal and family histories. One hundred and thirty‐five subjects were referred to the genetic counseling clinics and enrolled in the study. Full sequencing analysis of the BRCA1/2 gene showed 28 types of deleterious mutations in 36 subjects (26.7%), including 13 types of BRCA1 mutations in 17 subjects (12.6%) and 15 types of BRCA2 mutations in 19 subjects (14.1%). Subjects were classified into five groups and 22 subgroups according to their personal and family history of breast and/or ovarian cancer, and the prevalence of deleterious mutations was compared with previously reported data in non‐Ashkenazi individuals. Statistical analysis using the Mantel‐Haenszel test for groups I through IV revealed that the prevalence of Japanese subjects was significantly higher than that of non‐Ashkenazi individuals (P = 0.005, odds ratio 1.87, 95% confidence interval 1.22–2.88). Family history of the probands suffering from breast cancer indicated risk factors for the presence of deleterious mutations of BRCA1/2 as follows: (1) families with breast cancer before age 40 within second degree relatives (P = 0.0265, odds ratio 2.833, 95% confidence interval 1.165–7.136) and (2) families with bilateral breast cancer and/or ovarian cancer within second degree relatives (P = 0.0151, odds ratio 2.88, 95% confidence interval 1.25–6.64). (Cancer Sci 2008; 99: 1967–1976)
A UK‐based cost–utility analysis of radiofrequency ablation or oesophagectomy for the management of high‐grade dysplasia in Barrett’s oesophagus
Authors: Boger P. C. , Turner D. , Roderick P. , Patel P. 
Published: September 2010

Aliment Pharmacol Ther2010;32:1332–1342SummaryBackground In the UK, oesophagectomy is the current recommendation for patients with persistent high‐grade dysplasia in Barrett’s oesophagus. Radiofrequency ablation is an alternative new technology with promising early trial results.Aim To undertake a cost–utility analysis comparing these two strategies.Methods We constructed a Markov model to simulate the natural history of a cohort of patients with high‐grade dysplasia in Barrett’s oesophagus undergoing one of two treatment options: (i) oesophagectomy or (ii) radiofrequency ablation followed by endoscopic surveillance with oesophagectomy for high‐grade dysplasia recurrence or persistence.Results In the base case analysis, radiofrequency ablation dominated as it generated 0.4 extra quality of life years at a cost saving of £1902. For oesophagectomy to be the most cost‐effective option, it required a radiofrequency ablation treatment failure rate (high‐grade dysplasia persistence or progression to cancer) of >44%, or an annual risk of high‐grade dysplasia recurrence or progression to cancer in the ablated oesophagus of >15% per annum. There was an 85% probability that radiofrequency ablation remained cost‐effective at the NICE willingness to pay threshold range of £20 000–30 000.Conclusion Radiofrequency ablation is likely to be a cost‐effective option for high‐grade dysplasia in Barrett’s oesophagus in the UK.
ORIGINAL ARTICLE: A survey of the management of needlestick injuries from incapacitated patients in intensive care units*
Authors: Burrows L. A. , Padkin A. 
Published: September 2010

SummaryThe Human Tissue Act 2004 and Mental Capacity Act 2005 resulted in a change in the management of needlestick injuries sustained from incapacitated patients. It appears unlawful to test for blood‐borne viruses without a patient’s consent for the sole benefit of the healthcare worker. This survey of intensive care units within England, Wales and Northern Ireland investigated how needlestick injuries from incapacitated patients had been managed within the previous year. Of the 225 intensive care units surveyed, 99 (44%) responded. Sixty‐two (62.6%) reported a needlestick injury to a healthcare worker from an incapacitated patient. Thirty‐six (64.3%) patients were tested for blood‐borne viruses without consent. Sixteen (25.8%) patients tested positive for blood‐borne viruses. Only 19 (30.6%) healthcare workers took post‐exposure prophylaxis following the injury. These results show that needlestick injuries from incapacitated patients are common and that the majority of patients were tested for blood‐borne viruses without consent.
A comparative study of neotectonic basins across the Hellenic arc: the Messiniakos, Argolikos, Saronikos and Southern Evoikos Gulfs
Authors: Papanikolaou D. , Lykousis V. , Chronis G. , Pavlakis P. 
Published: September 2010

Abstract Detailed single‐channel continuous seismic reflection profiling data from four gulfs as well as onshore neotectonic investigations have allowed the study of the neotectonic structure of the Hellenic arc along a complete transverse section from its external area in the trench to the internal back‐arc area.Messiniakos Gulf is an asymmetric NW‐SE structure with considerable tilt towards the NE. It is the direct continuation of the continental slope from the trench to the island arc (Peloponnesus, Crete, Dodekannese). Argolikos Gulf is an almost symmetric NW‐SE graben occupying the northern edge of the Cretan back‐arc basin. Saronikos Gulf is a multi‐complex structure of a NW‐SE graben in the SW (Epidaurus Basin) and alternation of E‐W horsts and grabens in the North. Its neotectonic evolution is characterized by the Plio‐Quaternary volcanic arc activity. Southern Evoikos Gulf is a relatively shallow neotectonic graben in the back‐arc area at the northern prolongation of the Cycladic Platform.Each of the above neotectonic basins has its own characteristics which are probably due to their geodynamic position in the Hellenic arc. In general, there is a decrease in the neotectonic deformation, the sediment thickness and the sedimentation rates from SW to NE, going from the periphery to the core of the arc.
The Corinth‐Patras rift as the initial stage of continental fragmentation behind an active island arc (Greece)
Authors: Doutsos THEODOR , Kontopoulos NIKOLAOS , Poulimenos GEORGIOS 
Published: September 2010

AbstractDuring the migration of the back arc extension from central to western Greece the Corinth and Patras grabens are being formed. Orthogonal opening of these graben zones is accomplished by WNW listric normal faults and NNE transfer faults which produce an along‐axis fragmentation. The listric faults show an increase in the dip of the fault plane westwards as well as a decrease in the maximum extension rate from 50% to the east in the Corinth graben, to 10% to the west in the Patras graben. Similarly, towards the west, Plio‐Quaternary deposits become thinner whereas Pliocene sediments thin‐out indicating a westward rift propagation.As the back arc extension migrates westwards it is interacting or is being superimposed above another orthogonal fault system consisting of NNW and ENE normal faults. These faults have been formed during general uplift behind the orogenic front which has been migrating from western Greece to the Ionian islands. The ENE‐trending Rio graben which belongs to his orthogonal system connects the Patras graben to the Corinth graben and has subsequently been active as a transfer fault between them.Plio‐Quaternary geodynamic processes in central continental Greece are quite similar to those earlier processes observed in the central Aegean region which reflect the initial stage of continental break‐up behind a migrating orogenic front.
Estimating the slip rates of normal faults in the Great Basin, USA
Authors: DePolo C. M. , Anderson J. G. 
Published: September 2010

A reconnaissance slip‐rate‐estimation technique is needed for hundreds of uncharacterized normal faults in the Great Basin. We use the occurrence and/or absence of primary tectonic geomorphology, alluvial fault scarps and fault facets, to distinguished between categories of faults that have differences of orders of magnitudes in slip rate. Normal faults that lack alluvial fault scarps and fault facets (Type 3) have vertical slip rates on the order of 0.001 m kyr−1. Faults with alluvial fault scarps but that lack active fault facets (Type 2) have vertical slip rates on the order of 0.01 m kyr−1. Faults with active fault facets with a minimum height of 30 m (Type 1) are the most important faults in the Great Basin with respect to seismic hazard, tectonic deformation, and basin development and deposition. These faults generally have vertical slip rates of 0.1 m kyr−1 and faster. For better precision we have developed a relationship between vertical slip rate and maximum basal facet height: Log10 Sv=0.00248H−0.938 where Sv is vertical slip rate in m kyr−1 and H is maximum basal facet height in metres. The standard deviation of this relationship is 0.239, which corresponds to plus or minus a multiplicative factor of 1.7 in vertical slip rate.These criteria were used to estimate vertical slip rates for major normal faults in Nevada, USA. Based on the rates and orientations of these faults, seven Quaternary tectonic subprovinces are distinguished. The fastest faults (≥0.5 m kyr−1) are generally located in the Walker Lane belt, perhaps because of higher extension rates created by the addition of strike‐slip tectonics. Earthquake occurrence rates based on the faults in Nevada and their estimated slip rates are about a factor of two lower than historical earthquake rates.
The structural and sedimentological evolution of early synrift successions: the Middle Jurassic Tarbert Formation, North Sea
Authors: Davies S. J , Dawers N. H. , McLeod A. E. , Underhill J. R. 
Published: September 2010

ABSTRACTThis study addresses the complex relationship between an evolving fault population and patterns of synrift sedimentation during the earliest stages of extension. We have used 3D seismic and well data to examine the early synrift Tarbert Formation from the Middle–Late Jurassic northern North Sea rift basin. The Tarbert Formation is of variable thickness across the study area, and thickness variations define a number of 1‐ to 5‐km‐wide depocentres bounded by normal faults. Seismic reflections diverge towards the bounding faults indicating that the faults were active contemporaneous with the deposition of the formation. Many of these faults became inactive during later Heather Formation times. The preservation of the Tarbert Formation in both footwall and hangingwall locations demonstrates that, during the earliest synrift, the rate of deposition balanced the rate of tectonic subsidence. Local space generated by hangingwall subsidence was superimposed upon accommodation generated due to a regional rise in relative sea‐level. In basal Tarbert Formation times, transgression across the prerift coastal plain produced lagoons and bays, which became increasingly marine. During continued transgression, barrier islands moved landward across the drowned bays. In the southern part of our study area, shallow marine sediments are erosionally truncated by fluvial deposition. These fluvial systems were constrained by fault growth monoclines, and flowed parallel to the main faults. We illustrate that stratal architecture and facies distribution of early sedimentation is strongly influenced by the active short‐lived faults. Local depocentres adjacent to fault displacement maxima focused channel stacking and allowed the aggradation of thick shoreface successions. These depocentres formed early in the rift phase are not necessarily related to Late Jurassic – Early Cretaceous depocentres developed along the major linked normal fault systems.
Miocene–Recent tectonic and climatic controls on sediment supply and sequence stratigraphy: Canterbury basin, New Zealand
Authors: Lu Hongbo , Fulthorpe Craig S. , Mann Paul , Kominz Michelle A. 
Published: September 2010

AbstractThe well‐constrained seismic stratigraphy of the offshore Canterbury basin provides the opportunity to investigate long‐term changes in sediment supply related to the formation of a transpressive plate boundary (Alpine Fault). Reconstructions of the relative motion of the Australian and Pacific plates reveal divergence in the central Southern Alps prior to ∼20.1 Ma (chron 6o), followed by increasing average rates of convergence, with a marked increase after ∼6 Ma (late Miocene). A strike–slip component existed prior to 33.5 Ma (chron 13o) and perhaps as early as Eocene (45 Ma). However, rapid strike–slip motion (>30 mm yr−1) began at ∼20.1 Ma (chron 6o). Since ∼20.1 Ma there has been no significant change in the strike–slip component of relative plate motion.Sedimentation rates are calculated from individual sequence volumes that are then summed to represent sequence groups covering the same time periods as the tectonic reconstructions. Rates are relatively high (>22 mm yr−1), from 15 to ∼11.5 Ma (sequence group 1). Rates decrease to a minimum (<15 mm yr−1) during the ∼11.5–6 Ma interval (sequence group 2), followed by increased rates during the periods of ∼6–2.6 Ma (21 mm yr−1; group 3) and 2.6–0 Ma (∼25 mm yr−1; group 4). Good agreement between sedimentation and tectonic convergence rates in sequence groups 2–4 indicates that tectonism has been the dominant control on sediment supply to the Canterbury basin since ∼11.5 Ma. In particular, high sedimentation rates of 21 and ∼25 mm yr−1 in groups 3 and 4, respectively, may reflect increased plate convergence and uplift at the Southern Alps at ∼6 Ma. The early‐middle Miocene (∼15–11.5 Ma) high sedimentation rate (22 mm yr−1) correlates with low convergence rates (∼2 mm yr−1) and is mainly a response to global climatic and eustatic forcing.