bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disruption of playa–lacustrine depositional systems at the Permo-Triassic boundary: evidence from Vyazniki and Gorokhovets on the Russian Platform
Authors: Newell Andrew J. , Sennikov Andrey G. , Benton Michael J. , Molostovskaya Iya I. , Golubev Valeriy K. , Minikh Alla V. , Minikh Maxim G. 
Published: June 2010

Abstract:
Permo-Triassic sections at Vyazniki and Gorokhovets provide evidence on terrestrial events at, or close to, the Permo-Triassic boundary, the time of the largest ever mass extinction. The sedimentary succession records the overrun of a muddy playa–lacustrine depositional system by major channel belts transporting sand-grade sediments. Biostratigraphy of sections at Vyazniki and Gorokhovets (Zhukov Ravine) shows that this event occurred either at the very end of the Permian or 8 m above in the sections. The timing and nature of this event, which records increased sediment flux from the Ural Mountains, is closely comparable with that from the Southern Uralian Foreland Basin. The Vyazniki and Gorokhovets sections are 800 km from the mountain front and in a separate depositional basin, which strengthens the case that increased sediment flux from the Urals at the Permo-Triassic boundary is related to devegetation of upland catchments (increasing sediment yield) and a switch toward low-frequency but high-magnitude discharge events (increasing sediment delivery). The interbedding of fluvial and aeolian deposits provides further evidence for climatic instability and extremes in the Early Triassic.

Supplementary material:

Detailed reports on the ostracodes and fossil fish remains from the Zhukov Ravine sections are available at
http://www.geolsoc.org.uk/SUP18402
.
Multiple post-Caledonian exhumation episodes across NW Scotland revealed by apatite fission-track analysis
Authors: Holford Simon P. , Green Paul F. , Hillis Richard R. , Underhill John R. , Stoker Martyn S. , Duddy Ian R. 
Published: June 2010

Abstract:
The post-Caledonian exhumation history of NW Scotland is a controversial issue, with some studies advocating largely continual emergence whereas others suggest dominantly early Palaeogene plume-driven exhumation. Apatite fission-track analysis (AFTA) data for samples of Precambrian basement and Permian–Cretaceous sediments from onshore and offshore reveal multiple phases of post-Caledonian cooling: Triassic (beginning 245–225 Ma), Cretaceous (140–130 Ma; 110–90 Ma) and Cenozoic (65–60 Ma; 40–25 Ma; 15–10 Ma), all of which are interpreted at least in part as recording exhumation. Basement and sedimentary cover rocks display similar thermal histories, emphasizing the regional nature of these episodes and implying that sedimentary outliers represent the remnants of previously more extensive sequences. Significant thicknesses of Jurassic rocks may once have covered NW Scotland. Palaeocene palaeothermal effects are most pronounced in the vicinity of igneous centres, probably reflecting combined effects of heating by elevated heat flow, deeper burial and hydrothermal activity. Most of the region underwent kilometre-scale Neogene exhumation. Contrary to the common assumption of monotonic cooling and denudation histories, integration of geological evidence with AFTA data defines an episodic thermal history involving repeated cycles of burial and exhumation. We suggest that onshore passive margins and continental interiors may also best be characterized by similar histories.
Arity-generic datatype-generic programming
Authors: Weirich Stephanie , Casinghino Chris 
Published: June 2010

Some programs are doubly-generic. For example, map is datatype-generic in that many different data structures support a mapping operation. A generic programming language like Generic Haskell can use a single definition to generate map for each type. However, map is also arity-generic because it belongs to a family of related operations that differ in the number of arguments. For lists, this family includes repeat, map, zipWith, zipWith3, zipWith4, etc. With dependent types or clever programming, one can unify all of these functions together in a single definition.
However, no one has explored the combination of these two forms of genericity. These two axes are not orthogonal because the idea of arity appears in Generic Haskell: datatype-generic versions of repeat, map and zipWith have different arities of kind-indexed types. In this paper, we define arity-generic datatype-generic programs by building a framework for Generic Haskell-style generic programming in the dependently-typed programming language Agda 2.
The Climatology of the Middle Atmosphere in a Vertically Extended Version of the Met Office’s Climate Model. Part II: Variability
Authors: Osprey Scott M. , Gray Lesley J. , Hardiman Steven C. , Butchart Neal , Bushell Andrew C. , Hinton Tim J. 
Published: June 2010

Abstract
Stratospheric variability is examined in a vertically extended version of the Met Office global climate model. Equatorial variability includes the simulation of an internally generated quasi-biennial oscillation (QBO) and semiannual oscillation (SAO). Polar variability includes an examination of the frequency of sudden stratospheric warmings (SSW) and annular mode variability. Results from two different horizontal resolutions are also compared. Changes in gravity wave filtering at the higher resolution result in a slightly longer QBO that extends deeper into the lower stratosphere. At the higher resolution there is also a reduction in the occurrence rate of sudden stratospheric warmings, in better agreement with observations. This is linked with reduced levels of resolved waves entering the high-latitude stratosphere. Covariability of the tropical and extratropical stratosphere is seen, linking the phase of the QBO with disturbed NH winters, although this linkage is sporadic, in agreement with observations. Finally, tropospheric persistence time scales and seasonal variability for the northern and southern annular modes are significantly improved at the higher resolution, consistent with findings from other studies.
Coupled Land–Atmosphere Intraseasonal Variability of the West African Monsoon in a GCM
Authors: Lavender Sally L. , Taylor Christopher M. , Matthews Adrian J. 
Published: June 2010

Abstract
Recent observational studies have suggested a role for soil moisture and land–atmosphere coupling in the 15-day westward-propagating mode of intraseasonal variability in the West African monsoon. This hypothesis is investigated with a set of three atmospheric general circulation model experiments. 1) When soil moisture is fully coupled with the atmospheric model, the 15-day mode of land–atmosphere variability is clearly identified. Precipitation anomalies lead soil moisture anomalies by 1–2 days, similar to the results from satellite observations. 2) To assess whether soil moisture is merely a passive response to the precipitation, or an active participant in this mode, the atmospheric model is forced with a 15-day westward-propagating cycle of regional soil moisture anomalies based on the fully coupled mode. Through a reduced surface sensible heat flux, the imposed wet soil anomalies induce negative low-level temperature anomalies and increased pressure (a cool high). An anticyclonic circulation then develops around the region of wet soil, enhancing northward moisture advection and precipitation to the west. Hence, in a coupled framework, this soil moisture–forced precipitation response would provide a self-consistent positive feedback on the westward-propagating soil moisture anomaly and implies an active role for soil moisture. 3) In a final sensitivity experiment, soil moisture is again externally prescribed but with all intraseasonal fluctuations suppressed. In the absence of soil moisture variability there are still pronounced surface sensible heat flux variations, likely due to cloud changes, and the 15-day westward-propagating precipitation signal is still present. However, it is not as coherent as in the previous experiments when interaction with soil moisture was permitted. Further examination of the soil moisture forcing experiment in GCM experiment 2 shows that this precipitation mode becomes phase locked to the imposed soil moisture anomalies. Hence, the 15-day westward-propagating mode in the West African monsoon can exist independently of soil moisture; however, soil moisture and land–atmosphere coupling act to feed back on the atmosphere and further enhance and organize it.
Wake Measurements of a Multi-MW Wind Turbine with Coherent Long-Range Pulsed Doppler Wind Lidar
Authors: Käsler Yvonne , Rahm Stephan , Simmet Rudolf , Kühn Martin 
Published: June 2010

Abstract
Long-range Doppler wind light detection and ranging (lidar) measurements at a wind turbine were carried out for the first time. The turbine was of the type Areva M5000 and is located at a site near the coastline in Bremerhaven, in the northern part of Germany. This wind turbine is the prototype for the German offshore test site “alpha ventus” and has a rated power of 5 MW. Information about the ambient wind field before and after this multimegawatt wind turbine was obtained. In this paper the measurement technique is discussed and the results of measurements in the diurnal layer and in the stable nocturnal boundary layer are shown. The main focus of this work is to determine the reduction of the wind speed at certain distances downstream from the rotor.
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
Authors: Chauhan Jagat S , Mishra Nitish K , Raghava Gajendra PS 
Published: June 2010

AbstractBackgroundGuanosine triphosphate (GTP)-binding proteins play an important role in regulation of G-protein. Thus prediction of GTP interacting residues in a protein is one of the major challenges in the field of the computational biology. In this study, an attempt has been made to develop a computational method for predicting GTP interacting residues in a protein with high accuracy (Acc), precision (Prec) and recall (Rc).ResultAll the models developed in this study have been trained and tested on a non-redundant (40% similarity) dataset using five-fold cross-validation. Firstly, we have developed neural network based models using single sequence and PSSM profile and achieved maximum Matthews Correlation Coefficient (MCC) 0.24 (Acc 61.30%) and 0.39 (Acc 68.88%) respectively. Secondly, we have developed a support vector machine (SVM) based models using single sequence and PSSM profile and achieved maximum MCC 0.37 (Prec 0.73, Rc 0.57, Acc 67.98%) and 0.55 (Prec 0.80, Rc 0.73, Acc 77.17%) respectively. In this work, we have introduced a new concept of predicting GTP interacting dipeptide (two consecutive GTP interacting residues) and tripeptide (three consecutive GTP interacting residues) for the first time. We have developed SVM based model for predicting GTP interacting dipeptides using PSSM profile and achieved MCC 0.64 with precision 0.87, recall 0.74 and accuracy 81.37%. Similarly, SVM based model have been developed for predicting GTP interacting tripeptides using PSSM profile and achieved MCC 0.70 with precision 0.93, recall 0.73 and accuracy 83.98%.ConclusionThese results show that PSSM based method performs better than single sequence based method. The prediction models based on dipeptides or tripeptides are more accurate than the traditional model based on single residue. A web server "GTPBinder"http://www.imtech.res.in/raghava/gtpbinder/based on above models has been developed for predicting GTP interacting residues in a protein.
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-κB signaling-induced gene expression responses in inflammation
Authors: Peng Shih Chi , Wong David Shan Hill , Tung Kai Che , Chen Yan Yu , Chao Chun Cheih , Peng Chien Hua , Chuang Yung Jen , Tang Chuan Yi 
Published: June 2010

AbstractBackgroundSignal transduction is the major mechanism through which cells transmit external stimuli to evoke intracellular biochemical responses. Diverse cellular stimuli create a wide variety of transcription factor activities through signal transduction pathways, resulting in different gene expression patterns. Understanding the relationship between external stimuli and the corresponding cellular responses, as well as the subsequent effects on downstream genes, is a major challenge in systems biology. Thus, a systematic approach is needed to integrate experimental data and theoretical hypotheses to identify the physiological consequences of environmental stimuli.ResultsWe proposed a systematic approach that combines forward and reverse engineering to link the signal transduction cascade with the gene responses. To demonstrate the feasibility of our strategy, we focused on linking the NF-κB signaling pathway with the inflammatory gene regulatory responses because NF-κB has long been recognized to play a crucial role in inflammation. We first utilized forward engineering (Hybrid Functional Petri Nets) to construct the NF-κB signaling pathway and reverse engineering (Network Components Analysis) to build a gene regulatory network (GRN). Then, we demonstrated that the corresponding IKK profiles can be identified in the GRN and are consistent with the experimental validation of the IKK kinase assay. We found that the time-lapse gene expression of several cytokines and chemokines (TNF-α, IL-1, IL-6, CXCL1, CXCL2 and CCL3) is concordant with the NF-κB activity profile, and these genes have stronger influence strength within the GRN. Such regulatory effects have highlighted the crucial roles of NF-κB signaling in the acute inflammatory response and enhance our understanding of the systemic inflammatory response syndrome.ConclusionWe successfully identified and distinguished the corresponding signaling profiles among three microarray datasets with different stimuli strengths. In our model, the crucial genes of the NF-κB regulatory network were also identified to reflect the biological consequences of inflammation. With the experimental validation, our strategy is thus an effective solution to decipher cross-talk effects when attempting to integrate new kinetic parameters from other signal transduction pathways. The strategy also provides new insight for systems biology modeling to link any signal transduction pathways with the responses of downstream genes of interest.
Chromosome phylogeny of the subfamily Pitheciinae (Platyrrhini, Primates) by classic cytogenetics and chromosome painting
Authors: Finotelo Liane FM , Amaral Paulo JS , Pieczarka Julio C , de Oliveira Edivaldo HC , Pissinati Alcides , Neusser Michaela , Müller Stephan , Nagamachi Cleusa Y 
Published: June 2010

Abstract

Background
The New World monkey (Platyrrhini) subfamily Pitheciinae is represented by the genera Pithecia, Chiropotes and Cacajao. In this work we studied the karyotypes of Pithecia irrorata (2n = 48) and Cacajao calvus rubicundus (2n = 45 in males and 2n = 46 in females) by G- and C-banding, NOR staining and chromosome painting using human and Saguinus oedipus whole chromosome probes. The karyotypes of both species were compared with each other and with Chiropotes utahicki (2n = 54) from the literature.

Results
Our results show that members of the Pitheciinae have conserved several chromosome forms found in the inferred ancestral Platyrrhini karyotype (associations of human homologous segments 3a/21, 5/7a, 2b/16b, 8a/18, 14/15a and 10a/16a). Further, the monophyly of this subfamily is supported by three chromosomal synapomorphies (2a/10b, an acrocentric 15/14 and an acrocentric human 19 homolog). In addition, each species presents several autapomorphies. From this data set we established a chromosomal phylogeny of Pitheciinae, resulting in a single most parsimonious tree.

Conclusions
In our chromosomal phylogeny, the genus Pithecia occurred in a more basal position close to the inferred ancestor of Platyrrhini, while C. c. rubicundus and C. utahicki are closely related and are linked by exclusive synapomorphies.
High resolution mapping of trypanosomosis resistance loci Tir 2 and Tir 3 using F12 advanced intercross lines with major locus Tir 1 fixed for the susceptible allele
Authors: Nganga Joseph K , Soller Morris , Iraqi Fuad A 
Published: June 2010

Abstract

Background
Trypanosomosis is the most economically important disease constraint to livestock productivity in Africa. A number of trypanotolerant cattle breeds are found in West Africa, and identification of the genes conferring trypanotolerance could lead to effective means of genetic selection for trypanotolerance. In this context, high resolution mapping in mouse models are a promising approach to identifying the genes associated with trypanotolerance. In previous studies, using F2 C57BL/6J × A/J and C57BL/6J × BALB/cJ mouse resource populations, trypanotolerance QTL were mapped within a large genomic intervals of 20-40 cM to chromosomes MMU17, 5 and 1, and denoted Tir 1, Tir 2 and Tir 3 respectively. Subsequently, using F6 C57BL/6J × A/J and C57BL/6J × BALB/cJ F6 advanced intercross lines (AIL), Tir 1 was fine mapped to a confidence interval (CI) of less than 1 cM, while Tir 2 and Tir 3, were mapped within 5-12 cM. Tir 1 represents the major trypanotolerance QTL.

Results
In order to improve map resolutions of Tir 2 and Tir 3, an F12 C57BL/6J × A/J AIL population fixed for the susceptible alleles at Tir 1 QTL was generated. An F12 C57BL/6J × A/J AIL population, fixed for the resistant alleles at Tir 1 QTL was also generated to provide an additional estimate of the gene effect of Tir 1. The AIL populations homozygous for the resistant and susceptible Tir 1 alleles and the parental controls were challenged with T. congolense and followed for survival times over 180 days. Mice from the two survival extremes of the F12 AIL population fixed for the susceptible alleles at Tir 1 were genotyped with a dense panel of microsatellite markers spanning the Tir 2 and Tir 3 genomic regions and QTL mapping was performed. Tir 2 was fine mapped to less than 1 cM CI while Tir 3 was mapped to three intervals named Tir 3a, Tir 3b and Tir 3c with 95% confidence intervals (CI) of 6, 7.2 and 2.2 cM, respectively.

Conclusions
The mapped QTL regions encompass genes that are vital to innate immune response and can be potential candidate genes for the underlying QTL.
Does D3 surgery offer a better survival outcome compared to D1 surgery for gastric cancer? A result based on a hospital population of two decades as taking D2 surgery for reference
Authors: Zhang Hao , Liu Caigang , Wu Di , Meng Yi , Song Ruonan , Lu Ping , Wang Shubao 
Published: June 2010

Abstract

Background
We conducted a retrospective study in our hospital in which we compared D1 with D3 through D2 lymphadenectomy for gastric cancer in terms of morbidity, postoperative mortality, long-term survival after surgery.

Methods
567 patients who were performed curative intent between 1980 and 2003 were enrolled. 187 in the D1 group, 189 in the D2 group and 191 in the D3 group. Every procedure was verified by pathological analyses. The primary endpoints were 5-year overall survival.

Results
Median follow-up periods were 36 months and 60 months for D1 group and D3 group. Overall 5-year survival rate was significantly higher in patients underwent D3 surgery than in those performed D1 surgery (37.4% vs 48.7%; log-rank, p = 0.027). For the cases followed up to 120 months, the 10-year overall survival rate was 29% (95% CI, 22.1% to 35.9%) for the D1 group and 33.7% (95% CI, 26.6% to 40.8%) for the D3 group (log-rank, p = 0.005).

Conclusions
D1 surgery should be operated only for patients with Borrmann I disease. As D3 gastrectomy is associated with low mortality and adequate survival times when performed in selected institutions that have had sufficient experience with the operation and with postoperative management, we recommend D3 lymphadenectomy for patients with curable gastric cancer.
Peri-operative chemotherapy for the treatment of resectable liver metastases from colorectal cancer: A systematic review and meta-analysis of randomized trials
Authors: Wieser Martina , Sauerland Stefan , Arnold Dirk , Schmiegel Wolff , Reinacher-Schick Anke 
Published: June 2010

Abstract

Background
The role of peri-operative chemotherapy in patients with resected stage IV colorectal cancer (CRC) remains to be defined. This study was aimed at evaluating the effectiveness of peri-operative chemotherapy in patients with resected stage IV CRC by performing a meta-analysis of relevant trials.

Methods
We performed a literature search to identify trials comparing patients with stage IV CRC receiving peri-operative chemotherapy and surgery with patients undergoing surgery alone. The hazard ratio (HR) was estimated to assess any survival advantage of peri-operative chemotherapy.

Results
Eight trials conducted on a total of 1174 patients were identified by a literature search. In these trials, HR estimates suggested that peri-operative chemotherapy yielded no survival advantage over surgery alone (HR, 0.94; 95%CI, 0.8-1.10; p = 0.43). In a subset analysis on intra-arterial chemotherapy alone, no survival benefit was evident (HR, 1.0; 95% CI, 0.84-1.21; p = 0.96; I2 = 30%), whereas in the trials involving systemic chemotherapy, the difference between the groups approached statistical significance (HR, 0.74; 95% CI, 0.53-1.04; p = 0.08; I2 = 0%). Both peri-operative treatment groups had a significant recurrence-free survival benefit (HR, 0.78; 95% CI, 0.65-0.95; P = 0.01 for hepatic arterial infusion; and HR, 0.75; 95% CI, 0.62-0.91; p = 0.003 for systemic therapy). The toxicities of chemotherapy were acceptable in most trials.

Conclusions
This is the first meta-analysis demonstrating the importance of peri-operative chemotherapy in the treatment of resected stage IV CRC. Although the results must be carefully interpreted because of some limitations, critical issues were identified that must be resolved by future studies.
Associations between tamoxifen, estrogens, and FSH serum levels during steady state tamoxifen treatment of postmenopausal women with breast cancer
Authors: Gjerde Jennifer , Geisler Jürgen , Lundgren Steinar , Ekse Dagfinn , Varhaug Jan Erik , Mellgren Gunnar , Steen Vidar M , Lien Ernst A 
Published: June 2010

AbstractBackgroundThe cytochrome P450 (CYP) enzymes 2C19, 2D6, and 3A5 are responsible for converting the selective estrogen receptor modulator (SERM), tamoxifen to its active metabolites 4-hydroxy-tamoxifen (4OHtam) and 4-hydroxy-N-demethyltamoxifen (4OHNDtam, endoxifen). Inter-individual variations of the activity of these enzymes due to polymorphisms may be predictors of outcome of breast cancer patients during tamoxifen treatment. Since tamoxifen and estrogens are both partly metabolized by these enzymes we hypothesize that a correlation between serum tamoxifen and estrogen levels exists, which in turn may interact with tamoxifen on treatment outcome. Here we examined relationships between the serum levels of tamoxifen, estrogens, follicle-stimulating hormone (FSH), and also determined the genotypes of CYP2C19, 2D6, 3A5, and SULT1A1 in 90 postmenopausal breast cancer patients.MethodsTamoxifen and its metabolites were measured by liquid chromatography-tandem mass spectrometry. Estrogen and FSH levels were determined using a sensitive radio- and chemiluminescent immunoassay, respectively.ResultsWe observed significant correlations between the serum concentrations of tamoxifen,N-dedimethyltamoxifen, and tamoxifen-N-oxide and estrogens (p < 0.05). The genotype predicted CYP2C19 activity influenced the levels of both tamoxifen metabolites and E1.ConclusionsWe have shown an association between tamoxifen and its metabolites and estrogen serum levels. An impact of CYP2C19 predicted activity on tamoxifen, as well as estrogen kinetics may partly explain the observed association between tamoxifen and its metabolites and estrogen serum levels. Since the role of estrogen levels during tamoxifen therapy is still a matter of debate further prospective studies to examine the effect of tamoxifen and estrogen kinetics on treatment outcome are warranted.