bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of metabolic tumor volume: static versus dynamic FDG scans
Authors: Cheebsumon Patsuree , van Velden Floris HP , Yaqub Maqsood , Hoekstra Corneline J , Velasquez Linda M , Hayes Wendy , Hoekstra Otto S , Lammertsma Adriaan A , Boellaard Ronald 
Published: December 2011

Abstract

Background
Metabolic tumor volume assessment using positron-emission tomography [PET] may be of interest for both target volume definition in radiotherapy and monitoring response to therapy. It has been reported, however, that metabolic volumes derived from images of metabolic rate of glucose (generated using Patlak analysis) are smaller than those derived from standardized uptake value [SUV] images. The purpose of this study was to systematically compare metabolic tumor volume assessments derived from SUV and Patlak images using a variety of (semi-)automatic tumor delineation methods in order to identify methods that can be used reliably on (whole body) SUV images.

Methods
Dynamic [18F]-fluoro-2-deoxy-D-glucose [FDG] PET data from 10 lung and 8 gastrointestinal cancer patients were analyzed retrospectively. Metabolic tumor volumes were derived from both Patlak and SUV images using five different types of tumor delineation methods, based on various thresholds or on a gradient.

Results
In general, most tumor delineation methods provided more outliers when metabolic volumes were derived from SUV images rather than Patlak images. Only gradient-based methods showed more outliers for Patlak-based tumor delineation. Median measured metabolic volumes derived from SUV images were larger than those derived from Patlak images (up to 59% difference) when using a fixed percentage threshold method. Tumor volumes agreed reasonably well (< 26% difference) when applying methods that take local signal-to-background ratio [SBR] into account.

Conclusion
Large differences may exist in metabolic volumes derived from static and dynamic FDG image data. These differences depend strongly on the delineation method used. Delineation methods that correct for local SBR provide the most consistent results between SUV and Patlak images.
Low Energy Electron Point Source Microscopy of Two-Dimensional Carbon Nanostructures
Authors: Vieker Henning , Beyer André , Blank Holger , Weber Dirk Henning , Gerthsen Dagmar , Gölzhäuser Armin 
Published: December 2011

Abstract
1 nm thick carbon nanomembranes (CNMs) are investigated with Low Energy Electron Point Source (LEEPS) microscopy. A CNM consists of a freely suspended carbon film made from a cross-linked self-assembled monolayer (SAM). During thermal annealing the CNM transforms into nanocrystalline graphene.We determined the electron transmissivity of CNMs from the LEEPS images. After pyrolysis, the LEEPS images showed clear differences compared to pristine CNMs. Upon annealing above 800 ºC the LEEPS images exhibit distinct features that are related to the structural transition. A comparison of LEEPS images with transmission electron micrographs of the same regions and features demonstrates that both microscopic techniques reveal similar structural features.
High Resolution IR Spectroscopy of the C–H Stretch Bands of Benzene Monomer and Dimer in Helium Nanodroplets
Authors: Poerschke Torsten , Habig Daniel , Havenith Martina 
Published: December 2011

Abstract
The IR spectrum of benzene and benzene dimer embedded in superfluid helium droplets in the region of the C–H stretch vibration (3000–3110 cm-1) was observed. By analyzing the pressure dependence of the spectra it was possible to assign these spectra to benzene monomer and dimer.
Based on a comparison of the observed position of the dimer bands to experimental bands recorded in the gas phase and to theoretical frequency predictions the authors assign these to the tilted T-shaped benzene dimer structure. None of the other two possible structures (PD or PTS) were found. The above assignment is firm.
For the monomer, we find in helium nanodroplets a splitting of the ν
8+ν
19
combination band observed in the gas phase. We assign this to an additional Fermi resonance which is caused by the matrix shift in helium nanodroplets.
Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome
Authors: Torres Giovana A , Gong Zhiyun , Iovene Marina , Hirsch Cory D , Buell C Robin , Bryan Glenn J , Novák Petr , Macas Jiří , Jiang Jiming 
Published: December 2011

AbstractSubtelomeric domains immediately adjacent to telomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes. A common feature associated with subtelomeric regions in different eukaryotes is the presence of long arrays of tandemly repeated satellite sequences. However, studies on molecular organization and evolution of subtelomeric repeats are rare. We isolated two subtelomeric repeats, CL14 and CL34, from potato (Solanum tuberosum). The CL14 and CL34 repeats are organized as independent long arrays, up to 1-3 Mb, of 182 bp and 339 bp monomers, respectively. The CL14 and CL34 repeat arrays are directly connected with the telomeric repeats at some chromosomal ends. The CL14 repeat was detected at the subtelomeric regions among highly diverged Solanum species, including tomato (Solanum lycopersicum). In contrast, CL34 was only found in potato and its closely related species. Interestingly, the CL34 repeat array was always proximal to the telomeres when both CL14 and CL34 were found at the same chromosomal end. In addition, the CL34 repeat family showed more sequence variability among monomers compared with the CL14 repeat family. We conclude that the CL34 repeat family emerged recently from the subtelomeric regions of potato chromosomes and is rapidly evolving. These results provide further evidence that subtelomeric domains are among the most dynamic regions in eukaryotic genomes.
Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms inNeurospora crassa
Authors: McCluskey Kevin , Wiest Aric E , Grigoriev Igor V , Lipzen Anna , Martin Joel , Schackwitz Wendy , Baker Scott E 
Published: December 2011

AbstractClassical forward genetics has been foundational to modern biology, and has been the paradigm for characterizing the role of genes in shaping phenotypes for decades. In recent years, reverse genetics has been used to identify the functions of genes, via the intentional introduction of variation and subsequent evaluation in physiological, molecular, and even population contexts. These approaches are complementary and whole genome analysis serves as a bridge between the two. We report in this article the whole genome sequencing of eighteen classical mutant strains of Neurospora crassa and the putative identification of the mutations associated with corresponding mutant phenotypes. Although some strains carry multiple unique nonsynonymous, nonsense, or frameshift mutations, the combined power of limiting the scope of the search based on genetic markers and of using a comparative analysis among the eighteen genomes provides strong support for the association between mutation and phenotype. For ten of the mutants, the mutant phenotype is recapitulated in classical or gene deletion mutants in Neurospora or other filamentous fungi. From thirteen to 137 nonsense mutations are present in each strain and indel sizes are shown to be highly skewed in gene coding sequence. Significant additional genetic variation was found in the eighteen mutant strains, and this variability defines multiple alleles of many genes. These alleles may be useful in further genetic and molecular analysis of known and yet-to-be-discovered functions and they invite new interpretations of molecular and genetic interactions in classical mutant strains.
Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)
Authors: Zhu Chengsong , Li Xianran , Yu Jianming 
Published: December 2011

AbstractHigh-density array-based genome-wide association studies (GWAS) are complemented by exome sequencing and whole-genome resequencing-based association studies. Here we present a composite resequencing-based genome-wide association study (CR-GWAS) strategy that systematically exploits collective biological information and analytical tools for a robust analysis. We showcased the utility of this strategy by using Arabidopsis (Arabidopsis thaliana) resequencing data. Bioinformatic predictions of biological function alteration at each locus were integrated into the process of association testing of both common and rare variants for complex traits with a suite of statistics. Significant signals were then filtered with a priori candidate loci generated from genome database and gene network models to obtain a posteriori candidate loci. A probabilistic gene network (AraNet) that interrogates network neighborhoods of genes was then used to expand the filtering power to examine the significant testing signals. Using this strategy, we confirmed the known true positives and identified several new promising associations. Promising genes (AP1, FCA, FRI, FLC, FLM, SPL5, FY, and DCL2) were shown to control for flowering time through either common variants or rare variants within a diverse set of Arabidopsis accessions. Although many of these candidate genes were cloned earlier with mutational studies, identifying their allele variation contribution to overall phenotypic variation among diverse natural accessions is critical. Our rare allele testing established a greater number of connections than previous analyses in which this issue was not addressed. More importantly, our results demonstrated the potential of integrating various biological, statistical, and bioinformatic tools into complex trait dissection.
Polymorphism and Divergence in Two Willow Species,Salix viminalisL. andSalix schweriniiE. Wolf
Authors: Berlin Sofia , Fogelqvist Johan , Lascoux Martin , Lagercrantz Ulf , Rönnberg-Wästljung Ann Christin 
Published: December 2011

AbstractWe investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe.
SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery
Authors: Hammond Thomas M , Xiao Hua , Boone Erin C , Perdue Tony D , Pukkila Patricia J , Shiu Patrick K T 
Published: December 2011

AbstractIn Neurospora crassa, genes lacking a pairing partner during meiosis are suppressed by a process known as meiotic silencing by unpaired DNA (MSUD). To identify novel MSUD components, we have developed a high-throughput reverse-genetic screen for use with the N. crassa knockout library. Here we describe the screening method and the characterization of a gene (sad-3) subsequently discovered. SAD-3 is a putative helicase required for MSUD and sexual spore production. It exists in a complex with other known MSUD proteins in the perinuclear region, a center for meiotic silencing activity. Orthologs of SAD-3 include Schizosaccharomyces pombe Hrr1, a helicase required for RNAi-induced heterochromatin formation. Both SAD-3 and Hrr1 interact with an RNA-directed RNA polymerase and an Argonaute, suggesting that certain aspects of silencing complex formation may be conserved between the two fungal species.
Variable Transposition of Eight Maize Activator (Ac) Elements Located on the Short Arm of Chromosome 1
Authors: Sheridan William F 
Published: December 2011

Abstract
Eight Activator (Ac) transposable elements mapped to the maize chromosome arm 1S were assessed for Ac transposition rates. For each of the Ac stocks, plants homozygous for the single Ac element and the Ds reporter r1-sc:m3 on chromosome 10 were crossed as females by a homozygous r1-sc:m3 tester color-converted W22 line. The resulting ears produced mostly coarsely spotted kernels and a low frequency of either near-colorless fine-spotted kernels or nonspotted kernels. The relative frequency of these two types of near-colorless kernels differed among the eight Ac stocks. The extent to which increased Ac dosage results in nonspotted kernels may be Ac-specific. Although all of the Ac elements are in near-isogenic inbred W22 lines, they varied to a large extent in their transposition frequency. These differences might possibly result from structural differences among the Ac elements. Because one pair of Ac elements derived from Ac33 on chromosome arm 5S differed about 13-fold in transposition frequency and a second pair of Ac elements derived from Ac12 on chromosome arm 1S differed about 3-fold in transposition frequency, this is not a likely explanation for all eight Ac elements. The data presented here support the notion that the differences in transposition frequency of the eight Ac elements may be a reflection of variability in Ac transcription or accessibility of the transposase to the Ac element, resulting from differences in the chromatin environments wherein the Ac elements are located. This is the first report of variability in transposition rates among different Ac donor lines.
Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila
Authors: Fass Joseph N , Joshi Nikhil A , Couvillion Mary T , Bowen Josephine , Gorovsky Martin A , Hamilton Eileen P , Orias Eduardo , Hong Kyungah , Coyne Robert S , Eisen Jonathan A , Chalker Douglas L , Lin Dawei , Collins Kathleen 
Published: December 2011

Abstract
Genetically programmed DNA rearrangements can regulate mRNA expression at an individual locus or, for some organisms, on a genome-wide scale. Ciliates rely on a remarkable process of whole-genome remodeling by DNA elimination to differentiate an expressed macronucleus (MAC) from a copy of the germline micronucleus (MIC) in each cycle of sexual reproduction. Here we describe results from the first high-throughput sequencing effort to investigate ciliate genome restructuring, comparing Sanger long-read sequences from a Tetrahymena thermophila MIC genome library to the MAC genome assembly. With almost 25% coverage of the unique-sequence MAC genome by MIC genome sequence reads, we created a resource for positional analysis of MIC-specific DNA removal that pinpoints MAC genome sites of DNA elimination at nucleotide resolution. The widespread distribution of internal eliminated sequences (IES) in promoter regions and introns suggests that MAC genome restructuring is essential not only for what it removes (for example, active transposons) but also for what it creates (for example, splicing-competent introns). Consistent with the heterogeneous boundaries and epigenetically modulated efficiency of individual IES deletions studied to date, we find that IES sites are dramatically under-represented in the ∼25% of the MAC genome encoding exons. As an exception to this general rule, we discovered a previously unknown class of small (&lt;500 bp) IES with precise elimination boundaries that can contribute the 3′ exon of an mRNA expressed during genome restructuring, providing a new mechanism for expanding mRNA complexity in a developmentally regulated manner.
Double-Strand Break Repair and Holliday Junction Processing Are Required for Chromosome Processing in Stationary-Phase Escherichia coli Cells
Authors: Williams Ashley B , Hetrick Kyle M , Foster Patricia L 
Published: December 2011

Abstract
As nutrients are depleted and cell division ceases in batch cultures of bacteria, active processes are required to ensure that each cell has a complete copy of its genome. How chromosome number is manipulated and maintained in nondividing bacterial cells is not fully understood. Using flow cytometric analysis of cells from different growth phases, we show that the Holliday junction–processing enzymes RuvABC and RecG, as well as RecBCD, the enzyme complex that initiates DNA double-strand break repair, are required to establish the normal distribution of fluorescent peaks, which is commonly accepted to reflect the distribution of chromosome numbers. Our results reveal that these proteins are required for the proper processing of chromosomes in stationary phase.
Genome-Wide Association Analysis of Ischemic Stroke in Young Adults
Authors: Cheng Yu-Ching , O’Connell Jeffrey R , Cole John W , Stine O Colin , Dueker Nicole , McArdle Patrick F , Sparks Mary J , Shen Jess , Laurie Cathy C , Nelson Sarah , Doheny Kimberly F , Ling Hua , Pugh Elizabeth W , Brott Thomas G , Brown Robert D , Meschia James F , Nalls Michael , Rich Stephen S , Worrall Bradford , Anderson Christopher D , Biffi Alessandro , Cortellini Lynelle , Furie Karen L , Rost Natalia S , Rosand Jonathan , Manolio Teri A , Kittner Steven J , Mitchell Braxton D 
Published: December 2011

Abstract
Ischemic stroke (IS) is among the leading causes of death in Western countries. There is a significant genetic component to IS susceptibility, especially among young adults. To date, research to identify genetic loci predisposing to stroke has met only with limited success. We performed a genome-wide association (GWA) analysis of early-onset IS to identify potential stroke susceptibility loci. The GWA analysis was conducted by genotyping 1 million SNPs in a biracial population of 889 IS cases and 927 controls, ages 15–49 years. Genotypes were imputed using the HapMap3 reference panel to provide 1.4 million SNPs for analysis. Logistic regression models adjusting for age, recruitment stages, and population structure were used to determine the association of IS with individual SNPs. Although no single SNP reached genome-wide significance (P &lt; 5 × 10−8), we identified two SNPs in chromosome 2q23.3, rs2304556 (in FMNL2; P = 1.2 × 10−7) and rs1986743 (in ARL6IP6; P = 2.7 × 10−7), strongly associated with early-onset stroke. These data suggest that a novel locus on human chromosome 2q23.3 may be associated with IS susceptibility among young adults.
Efficacy of Two Different CHX-Containing Desensitizers: A Controlled Double-Blind Study
Authors: Drebenstedt S , Zapf A , Rödig T , Mausberg RF , Ziebolz D 
Published: December 2011

Clinical RelevanceCHX-containing desensitizers are used for treatment of hypersensitive teeth. This positive effect shows a durability of 3-month.
SEM Analysis of Hybrid Layer and Bonding Interface After Chlorhexidine Use
Authors: Lafuente D 
Published: December 2011

Clinical Relevance
More studies suggest that the bond between composite and dentin degrades over time because of the action of matrix metalloproteinase on collagen fibrils left unprotected by acid etching. Clinical actions should be taken to prevent this from happening and thus the failure of what should be a very long-term restoration.
Dynamiques démographiques et dimensions géographiques des populations africaines
Authors: Charbit Yves , Régnard Corinne 
Published: December 2011

Demographic Dynamics and geographical Patterns of African Populations.

Whereas Latin American and Asian demographic transitions are well advanced, differences between African sub-regions remain important.
This paper assesses changes in the trends of mortality and fertility and the influence of urbanization on both variables.
A regional analysis shows that contrarily to the theory of demographic transition, urbanization does not necessarily induce a decline of fertility and of mortality. Other factors must be taken into account, for instance the supply of health care.
Where the Muezzin calls. Culturalisation of a local conflict in the context of ethnic change in the Ruhr Conurbation / L'appel du muezzin. Conflit culturel et changement ethnique dans la Ruhr
Authors: Pott Andreas , Thieme Günter 
Published: December 2011

The urban conflict of the call of the muezzin in Dortmund is examined as an example of a new type of social conflicts in a society experiencing population changes due to immigration. The article aims at questioning the way the local dispute is commonly perceived as a cultural conflict. To achieve that a mixed methodology is applied. Using quantitative data the demographic and spatial changes of the local context is analysed. Against this background the authors try to reconstruct the central arguments of the opponents and the supporters of the call and examine how the local immigration context and cultural discourses are used as social
resources.
Les mises en scène des martyrs dans les cimetières de village au Liban Sud
Authors: Chaib Kinda 
Published: December 2011

Résumé L’article étudie les usages politiques du groupe « martyrs » dans le Liban contemporain à partir d’une analyse sémiotique de cimetières du Sud chiite du pays. Lieux de mémoire en train de se faire, les cimetières se révèlent être un site d’observation privilégié pour décortiquer les processus de construction d’un groupe. L’article donne notamment à voir le travail d’homogénéisation orchestré par les structures partisanes en lien permanent avec des formes de résistance locales.
The history of dipterology at the Canadian National Collection of Insects, with special reference to theManual of Nearctic Diptera
Authors: Cumming Jeffrey M. , Sinclair Bradley J. , Brooks Scott E. , O'Hara James E. , Skevington Jeffrey H. 
Published: December 2011

AbstractThe history of Diptera research at the Canadian National Collection of Insects is briefly outlined. Short biographic sketches of the coordinators of theManual of Nearctic Dipteraare given and the development of the Manual project is presented to provide background on their achievements. Lists of publications by each of the coordinators and of patronyms honouring them are provided. This Festschrift honours the remarkable contributions of the coordinators, J. Frank McAlpine, Bobbie V. Peterson, Guy E. Shewell, Herbert J. Teskey, J. Richard Vockeroth, and D. Monty Wood.
Docosia adustasp. nov. (Diptera: Mycetophilidae) from the Colombian Andes: a Holarctic element in northwestern South America
Authors: Oliveira Sarah Siqueira , de Souza Amorim Dalton 
Published: December 2011

AbstractA third Neotropical species of the genusDocosiaWinnertz is described from the Colombian Andes. Three males and four females ofD. adusta sp. nov.from Cundinamarca, Colombia, collected at 3600m elevation were examined. Detailed illustrations of the male and female terminalia are presented and morphological differences in relation to those of other species of the genus are discussed. The relationships between Holarctic and Neotropical species withinDocosiaare discussed and overlap of circumantarctic, tropical, and Nearctic elements in the northern Andes is considered.
The genus Chrysopilus in New Caledonia (Diptera: Rhagionidae)
Authors: Webb Donald W. 
Published: December 2011

AbstractSeventeen new species of Chrysopilus Macquart are described from New Caledonia with illustrations of the male head, wing, and genitalia. The new species are C. bicoloratus sp. nov., C. brunneabdominalis sp. nov., C. caliginosus sp. nov., C. chazeaui sp. nov., C. everti sp. nov., C. irwini sp. nov., C. frankmcalpinei sp. nov., C. mandjelia sp. nov., C. melinus sp. nov., C. noumea sp. nov., C. petersoni sp. nov., C. plautifrons sp. nov., C. sarramea sp. nov., C. shewelli sp. nov., C. teskeyi sp. nov., C. vockerothi sp. nov., and C. woodi sp. nov. Keys are provided to identify the species from New Caledonia.