bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drilling, Sampling, and Monitoring the Alpine Fault: Deep Fault Drilling Project—Alpine Fault, New Zealand; Franz Josef, New Zealand, 22–28 March 2009
Authors: Townend John 
Published: September 2009

Several fundamental geological and geophysical phenomena are associated with the midcrust. These include the transitions from brittle to ductile behavior and from unstable to stable frictional sliding; earthquake nucleation; maximum crustal stresses; and mineralization associated with permeable fractures. However, knowledge of deformation, seismogenesis, and mineralization in the midcrust is based largely on remote geophysical observations of active faults and direct geological observations of fossil faults.The Alpine Fault is a major dextral‐reverse fault that is thought to fail in large earthquakes (Mw ≈ 7.9) every 200–400 years and to have last ruptured in 1717 C.E. Ongoing uplift has rapidly exhumed a crustal section from 20‐to 30‐kilometer depths, yielding a young (<∼1‐million‐year‐old), well‐preserved sample of structures currently active at depth. The Deep Fault Drilling Project (DFDP) proposes to drill, sample, and monitor the Alpine Fault to better understand processes of rock deformation, seismogenesis, and mineralization.
AGU International Award Recognizes Outstanding Science in Developing Countries
Authors: Urrtia Jaime , Cazenave Anny , Brown Laurie , Chao Ben , Fraser Brian , Mesa Oscar , Muhongo Sospeter , Perillo Gerardo M. E. 
Published: September 2009

One of AGU's major programs is its honors program, which includes the Union medals and awards, fellowships, and section and focus group awards. The program seeks to recognize outstanding contributions made by AGU members and other individuals to the advancement of the Earth and space sciences; service to the community; and excellence in education, outreach, and science journalism.The International Award, the most recent addition to the Union's honors program, this year was presented for the third time, and nominations are being sought for the 2010 award. This award for international research cooperation was established to recognize an individual scientist or a small team for making an outstanding contribution to furthering the Earth and space sciences and using science for the benefit of society while laboring under adverse circumstances with limited resources in less favored nations.
Tomorrow's AGU: Building a Foundation for Good Governance
Authors: Grove Timothy L. 
Published: September 2009

In May, the AGU Council voted unanimously to create a 16‐member board of directors to oversee the business of the Union, and to expand the Council beyond section leadership to include focus group and committee leaders concentrating on matters of science and related Union activities such as AGU publications, meetings, and awards and honors (see Eos, 90(25), 213, 23 June 2009). This fall, the AGU membership will be asked to vote on these important changes.The Council action followed careful deliberation and reflects the recommendations of the Future Focus Task Force, which was formed to answer the question, “How will AGU need to change the way it does business to achieve its strategic vision and mission and remain a preeminent scientific society?”
International Arctic Sea Ice Monitoring Program Continues Into Second Summer
Authors: Overland James , Eicken Hajo , Meier Walt , Wiggins Helen 
Published: September 2009

Rapid and extreme environmental changes are occurring in the Arctic. To increase the understanding of these changes, a Web‐based Sea Ice Outlook program that was initiated in May 2008 has continued for a second summer in 2009 (http://www.arcus.org/search/seaiceoutlook). Here the term “outlook” refers to a procedure where investigators were asked in early June to provide projections of the mean sea ice extent for September, and to explain the rationale for their estimates.The outlook, initiated by the Study of Environmental Arctic Change (SEARCH), was developed in response to the dramatic decrease in the areal extent of sea ice in summer 2007, when the extent dropped to a value of 39% below the average sea ice extent for 1979–1999 and 23% below the previous record minimum extent in 2005 (Figure 1). An effective response to such radical changes in sea ice extent requires enhanced, rapid communication within the Arctic science community to observe and understand Arctic processes as new information becomes available.
A dictionary to identify small molecules and drugs in free text
Authors: Hettne Kristina M. , Stierum Rob H. , Schuemie Martijn J. , Hendriksen Peter J. M. , Schijvenaars Bob J. A. , Mulligen Erik M. van , Kleinjans Jos , Kors Jan A. 
Published: September 2009

AbstractMotivation: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers.Results: We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB and ChemIDplus. Rule-based term filtering, manual check of highly frequent terms and disambiguation rules were applied. We tested the combined dictionary and the dictionaries derived from the individual resources on an annotated corpus, and conclude the following: (i) each of the different processing steps increase precision with a minor loss of recall; (ii) the overall performance of the combined dictionary is acceptable (precision 0.67, recall 0.40 (0.80 for trivial names); (iii) the combined dictionary performed better than the dictionary in the chemical recognizer OSCAR3; (iv) the performance of a dictionary based on ChemIDplus alone is comparable to the performance of the combined dictionary.Availability: The combined dictionary is freely available as an XML file in Simple Knowledge Organization System format on the web site http://www.biosemantics.org/chemlist.Contact: k.hettne@erasmusmc.nlSupplementary information: Supplementary data are available at Bioinformatics online.
3D-SURFER: software for high-throughput protein surface comparison and analysis
Authors: La David , Esquivel-Rodríguez Juan , Venkatraman Vishwesh , Li Bin , Sael Lee , Ueng Stephen , Ahrendt Steven , Kihara Daisuke 
Published: September 2009

Abstract
Summary: We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites as well as protrusions and flat regions can also be identified and visualized.
Availability: 3D-SURFER is a web application that can be freely accessed from: http://dragon.bio.purdue.edu/3d-surfer
Contact: dkihara@purdue.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
Authors: Shen Ronglai , Olshen Adam B. , Ladanyi Marc 
Published: September 2009

AbstractMotivation: The molecular complexity of a tumor manifests itself at the genomic, epigenomic, transcriptomic and proteomic levels. Genomic profiling at these multiple levels should allow an integrated characterization of tumor etiology. However, there is a shortage of effective statistical and bioinformatic tools for truly integrative data analysis. The standard approach to integrative clustering is separate clustering followed by manual integration. A more statistically powerful approach would incorporate all data types simultaneously and generate a single integrated cluster assignment.Methods: We developed a joint latent variable model for integrative clustering. We call the resulting methodology iCluster. iCluster incorporates flexible modeling of the associations between different data types and the variance–covariance structure within data types in a single framework, while simultaneously reducing the dimensionality of the datasets. Likelihood-based inference is obtained through the Expectation–Maximization algorithm.Results: We demonstrate the iCluster algorithm using two examples of joint analysis of copy number and gene expression data, one from breast cancer and one from lung cancer. In both cases, we identified subtypes characterized by concordant DNA copy number changes and gene expression as well as unique profiles specific to one or the other in a completely automated fashion. In addition, the algorithm discovers potentially novel subtypes by combining weak yet consistent alteration patterns across data types.Availability: R code to implement iCluster can be downloaded at http://www.mskcc.org/mskcc/html/85130.cfmContact: shenr@mskcc.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Genome analysis with inter-nucleotide distances
Authors: Afreixo Vera , Bastos Carlos A. C. , Pinho Armando J. , Garcia Sara P. , Ferreira Paulo J. S. G. 
Published: September 2009

Abstract
Motivation: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis. Several mapping schemes have been used in the past, but they seem unrelated to any intrinsic characteristic of DNA. The objective of this work was to find a mapping scheme directly related to DNA characteristics and that would be useful in discriminating between different species. Mathematical models to explore DNA correlation structures may contribute to a better knowledge of the DNA and to find a concise DNA description.
Results: We developed a methodology to process DNA sequences based on inter-nucleotide distances. Our main contribution is a method to obtain genomic signatures for complete genomes, based on the inter-nucleotide distances, that are able to discriminate between different species. Using these signatures and hierarchical clustering, it is possible to build phylogenetic trees. Phylogenetic trees lead to genome differentiation and allow the inference of phylogenetic relations. The phylogenetic trees generated in this work display related species close to each other, suggesting that the inter-nucleotide distances are able to capture essential information about the genomes. To create the genomic signature, we construct a vector which describes the inter-nucleotide distance distribution of a complete genome and compare it with the reference distance distribution, which is the distribution of a sequence where the nucleotides are placed randomly and independently. It is the residual or relative error between the data and the reference distribution that is used to compare the DNA sequences of different organisms.
Contact: vera@ua.pt
Effect of Storage Temperature for Paddy on Consumer Perception of Cooked Rice
Authors: Jang Eun‐Hee , Lim Seung‐Taik , Kim Sang‐Sook 
Published: September 2009

ABSTRACTEffect of storage temperature (ST) (5, 15, and 25°C) for paddy on the consumer perception of cooked rice (CR) was investigated with six major rice cultivars in Korea (Ilmibyeo, Chucheongbyeo, Ilpumbyeo, Hwayeongbyeo, Nampyeongbyeo, and Odaebyeo) after 12 months of storage. Germination rate (GR) of the paddy, grading characteristics (percentages of head rice, broken kernels, damaged kernels, colored kernels and chalky kernels) of milled rice (MR) kernels, texture profile analysis (hardness, springiness, cohesiveness, adhesiveness, and chewiness) and color (L*, a*, and b*) of CR were measured. Also, consumer testing on CR was done with 108 consumers. Consumers evaluated acceptability for odor, appearance, taste, texture, and overall purchase intent, and willingness to pay (WTP) of CR. After 12 months of storage, physicochemical characteristics of MR and CR were significantly different depending on ST. The significant difference among three ST of paddy was noted for GR, color b* value, fat acidity of MR, and overall consumer acceptability of CR. The GR was constant during 12 months of storage at 5°C, whereas a significant decrease of GR was noted for all six cultivars within 12 months of storage at 25°C. The average WTP for rice stored at 5°C for 12 months was $U.S. 45.68/20 kg, whereas WTP for rice stored at 15°C and 25°C were $U.S. 44.19/20 kg and $U.S. 41.87/20 kg, respectively, implying the importance of ST on grain quality and product value by consumers. Overall consumer acceptability had high correlation coefficient with WTP (r = 0.985). Overall consumer acceptability had highest correlation with GR of paddy (r = 0.861), followed by b* value of CR (r = –0.826), fat acidity (r = –0.768), cohesiveness (r = 0.733), and hardness (r = –0.650) of CR by TA, implying GR of paddy and b* value of CR could be used as indicators for eating quality of rice.
Sensory Evaluation of Barley Chocolate Chip Cookies by Consumers with Different Demographic Background and Eating Patterns
Authors: Omary María Botero , Rosentrater Kurt A. , Lewis Douglas S. , Arndt Elizabeth , Frost Diana J. , Winstone Lauren M. 
Published: September 2009

ABSTRACTHealth organizations have recommended an increase in consumption of whole grains, total dietary fiber, and soluble fiber to help reduce the potential risk factor for the development of type‐2 diabetes, obesity, and cardiovascular disease, among others. The purpose of this project was to determine the sensory characteristics of chocolate chip (CC) cookies containing a high‐soluble fiber whole barley flour (HSFWB). Cookies with 0, 30, 50, and 70% HSFWB were evaluated for appearance, color, flavor, texture, and overall acceptability using a 9‐point hedonic scale. Forty‐nine students, faculty, and staff tested the cookies on three different days. Demographic and behavioral data on age, gender, ethnicity, frequency of eating CC cookies, daily effort to consume fiber (FD), consumption of reduced‐fat (RF) cookies, and texture preference (TP) of CC cookies were collected. The 50% HSFWB cookie could be potentially marketed among older consumers (22+), males, Hispanics, individuals who consume CC cookies at least once a week, those making a FD in their diet, persons who consume RF cookies, as well as those who have no TP for CC cookies. A response surface relating flavor and texture to overall acceptability produced almost equivalent results to the multivariate PLS results in terms of predicting overall acceptability, which facilitates analysis and interpretation.
Qualitative Zymographic Studies of Major Proteinases from Malted Sorghum (Sorghum bicolor L.) and Effects of Cultivar
Authors: Mokhawa Gaone , Ralefala Malebogo P. , Bulawayo Bernard B. , Ezeogu Lewis I. 
Published: September 2009

ABSTRACTProteolysis during cereal germination is vital both to seedling growth and the success of commercial malting and brewing. In this study, proteinases in proteolytic extracts from seeds and germinated grains of 11 Botswana sorghum cultivars were analyzed and partially characterized by one‐dimensional electrophoresis on SDS‐PAGE gels containing incorporated gelatin. Proteinase polymorphism was detected in both germinated and ungerminated sorghum grains. Fifteen distinct proteinase bands, with Mr values of 27,000–100,000 were detected in sorghum malt extract, while ungerminated sorghum displayed a maximum of four bands (Mr ≈ 78,000–100,000). Band numbers and identity varied markedly according to cultivar. More proteinase bands were detected at pH 4.6, than at pH 6.2 and 7.0, suggesting pH optima considerably below neutrality. Cysteine‐proteinases constituted a higher proportion (9 of 15) of the detected sorghum malt proteinases and were most detectable at pH 4.6. Multiple representatives were also detected for both serine‐ and metallo‐proteinases, although these were more active at pH 6.2 and 7.0. 1‐10 Phenanthroline inhibited malt metallo‐proteinase more strongly than EDTA, suggesting that these enzymes were most probably zinc‐dependent. Aspartyl‐proteinases were not detected, probably because of the substrate employed. Results indicate that the sorghum proteinase system is complex.
A Modified Extensigraph Method for Evaluating Dough Properties of Hard Wheat Breeding Lines
Authors: Chen R. Y. , Seabourn B. W. , Xie F. , Herald T. J. 
Published: September 2009

ABSTRACTA modified extensigraph method reduced sample quantity to 100 g from 300 g and testing time by half with easy dough preparation compared to the AACC standard extensigraph method, which challenges wheat breeding programs where the sample size is small and evaluations of large numbers of samples are demanded. Correlation coefficients (r) for 93 pairs of each of six extensigraph dough characteristics of 31 different tested wheat samples were r = 0.95 for resistance‐to‐extension, r = 0.80 for extensibility, r = 0.93 for ratio of resistance‐to‐extension to extensibility, r = 0.92 for ratio of maximum resistance‐to‐extension to extensibility, and r = 0.81 for area under the curve (energy). Correlation coefficients for the measurements of extensigraph dough characteristics at each of three rest‐time tests between the modified and standard methods were significant. Some dough mixing characteristics and bake tests correlated better with dough extension characteristics when determined by the modified method. Repeatability of the modified method test was good. The modified extensigraph method can be a useful alternative to the standard method for the milling and baking industries, crop quality surveys, and wheat quality research.
Stable Transcription Activities Dependent on an Orientation of Tam3 Transposon Insertions intoAntirrhinumand Yeast Promoters Occur Only within Chromatin
Authors: Uchiyama Takako , Fujino Kaien , Ogawa Takashi , Wakatsuki Akihito , Kishima Yuji , Mikami Tetsuo , Sano Yoshio 
Published: September 2009

AbstractTransposon insertions occasionally occur in the promoter regions of plant genes, many of which are still capable of being transcribed. However, it remains unclear how transcription of such promoters is able to occur. Insertion of the Tam3 transposon into various genes of Antirrhinum majus can confer leaky phenotypes without its excision. These genes, named Tam3-permissible alleles, often contain Tam3 in their promoter regions. Two alleles at different anthocyanin biosynthesis loci, nivearecurrens∷Tam3 (nivrec) and pallidarecurrens∷Tam3 (palrec), both contain Tam3 at a similar position immediately upstream of the promoter TATA-box; however, these insertions had different phenotypic consequences. Under conditions where the inserted Tam3 is immobilized, the nivrec line produces pale red petals, whereas the palrec line produces no pigment. These pigmentation patterns are correlated with the level of transcripts from the nivrec or palrec alleles, and these transcriptional activities are independent of DNA methylation in their promoter regions. In nivrec, Tam3 is inserted in an orientation that results in the 3′ end of Tam3 adjacent to the 5′ region of the gene coding sequence. In contrast, the palrec allele contains a Tam3 insertion in the opposite orientation. Four of five different nonrelated genes that are also Tam3-permissible alleles and contain Tam3 within the promoter region share the same Tam3 orientation as nivrec. The different transcriptional activities dependent on Tam3 orientation in the Antirrhinum promoters were consistent with expression of luciferase reporter constructs introduced into yeast chromosomes but not with transient expression of these constructs in Antirrhinum cells. These results suggest that for Tam3 to sustain stable transcriptional activity in various promoters it must be embedded in chromatin.
Deletion-Based Reverse Genetics in Medicago truncatula
Authors: Rogers Christian , Wen Jiangqi , Chen Rujin , Oldroyd Giles 
Published: September 2009

Abstract
The primary goal of reverse genetics, the identification of null mutations in targeted genes, is achieved through screening large populations of randomly mutagenized plants. T-DNA and transposon-based mutagenesis has been widely employed but is limited to species in which transformation and tissue culture are efficient. In other species, TILLING (for Targeting Induced Local Lesions IN Genomes), based on chemical mutagenesis, has provided an efficient method for the identification of single base pair mutations, only 5% of which will be null mutations. Furthermore, the efficiency of inducing point mutations, like insertion-based mutations, is dependent on target size. Here, we describe an alternative reverse genetic strategy based on physically induced genomic deletions that, independent of target size, exclusively recovers knockout mutants. Deletion TILLING (De-TILLING) employs fast neutron mutagenesis and a sensitive polymerase chain reaction-based detection. A population of 156,000 Medicago truncatula plants has been structured as 13 towers each representing 12,000 M2 plants. The De-TILLING strategy allows a single tower to be screened using just four polymerase chain reaction reactions. Dual screening and three-dimensional pooling allows efficient location of mutants from within the towers. With this method, we have demonstrated the detection of mutants from this population at a rate of 29% using five targets per gene. This De-TILLING reverse genetic strategy is independent of tissue culture and efficient plant transformation and therefore applicable to any plant species. De-TILLING mutants offer advantages for crop improvement as they possess relatively few background mutations and no exogenous DNA.
A Systems-Level Analysis of the Effects of Light Quality on the Metabolism of a Cyanobacterium
Authors: Singh Abhay K. , Bhattacharyya-Pakrasi Maitrayee , Elvitigala Thanura , Ghosh Bijoy , Aurora Rajeev , Pakrasi Himadri B. 
Published: September 2009

Abstract
Photosynthetic organisms experience changes in light quantity and light quality in their natural habitat. In response to changes in light quality, these organisms redistribute excitation energy and adjust photosystem stoichiometry to maximize the utilization of available light energy. However, the response of other cellular processes to changes in light quality is mostly unknown. Here, we report a systematic investigation into the adaptation of cellular processes in Synechocystis species PCC 6803 to light that preferentially excites either photosystem II or photosystem I. We find that preferential excitation of photosystem II and photosystem I induces massive reprogramming of the Synechocystis transcriptome. The rewiring of cellular processes begins as soon as Synechocystis senses the imbalance in the excitation of reaction centers. We find that Synechocystis utilizes the cyclic photosynthetic electron transport chain for ATP generation and a major part of the respiratory pathway to generate reducing equivalents and carbon skeletons during preferential excitation of photosystem I. In contrast, cytochrome c oxidase and photosystem I act as terminal components of the photosynthetic electron transport chain to produce sufficient ATP and limited amounts of NADPH and reduced ferredoxin during preferential excitation of photosystem II. To overcome the shortage of NADPH and reduced ferredoxin, Synechocystis preferentially activates transporters and acquisition pathways to assimilate ammonia, urea, and arginine over nitrate as a nitrogen source. This study provides a systematic analysis of cellular processes in cyanobacteria in response to preferential excitation and shows that the cyanobacterial cell undergoes significant adjustment of cellular processes, many of which were previously unknown.