bluuebunny/crossref_metadata_2025_split huggingface dataset:
12 The Abolition of Nuclear Armouries?
Authors: Quinlan Michael 
Published: May 2009

Abstract
This chapter looks at the idea of abolishing all nuclear armouries, observing that both extremes of debate about this often oversimplify the issues, but that the NPT-recognized nuclear-weapon possessor states have all in the past undertaken to accept abolition as an ultimate goal. It then notes that any path toward it, envisaging the abandonment of the contribution which nuclear weapons have probably made to the absence of major war between advanced powers since 1945, must tackle both deep political issues and complex technical problems—it will not suffice for study to focus just upon the latter. This chapter sketches in outline a range of issues in both categories, and argues that those who believe in abolition and those who do not could usefully make common cause in supporting study work to deepen understanding about avenues, obstacles, and implications.
1 The Nuclear Revolution
Authors: Quinlan Michael 
Published: May 2009

Abstract
This chapter starts with the destruction of Hiroshima and Nagasaki by nuclear weapons in 1945, to terminate World War II. It considers what people at the time thought about the significance of this, and how they came to see that war-prevention had henceforth to be the cardinal rule. It discusses how strategists and planners had to transform their ideas radically—and sometimes with difficulty—to the reality that the new weapons created the reductio ad absurdum of all-out warfare. It suggests that scientific advance anyway made this inevitable sooner or later, by one route or another, as policies need to recognize. It considers what rational use nuclear weapons can have, and underscores that nuclear risk cannot be neatly sealed off but permeates all substantial armed conflict between major advanced powers.
8 Arms Racing, Costs, and Arms Control
Authors: Quinlan Michael 
Published: May 2009

Abstract
This chapter first discusses whether the term ‘arms race’ is accurately applied to the history of nuclear-armoury development, and whether the costs of such development have been disproportionate to their value. It then examines the contribution which arms control agreements can make to reducing cost, risk, and uncertainty in the stable management of nuclear deterrence. It illustrates from the Cold War period some of the complications, both political and technical, that can arise in the shaping of such agreements, and the difficulty of including smaller armouries like that of Britain in formal limitation bargains. It next considers what future there is for bilateral US/Russia deals, and finally notes the value of nuclear-weapon-free zones and certain treaties constraining the deployment of nuclear weapons into new environments.
11 Nuclear Weapons in South Asia
Authors: Quinlan Michael 
Published: May 2009

Abstract
This chapter first recapitulates the history of Indian and Pakistani approaches to nuclear-weapon capability, leading up to the 1998 explosive tests. It considers the significance of the 1999 Kargil crisis and the 2001–2 mobilization stand-off, and notes the damaging Pakistani episode of A. Q. Khan's ‘nuclear black market’. It summarizes what is publicly known about the nuclear doctrines and operational capabilities of the two countries, and notes the complication of achieving war-prevention stability amid the asymmetries between them. It observes that recent relaxations in tension, as over Kashmir, are not irreversible, and posits a set of principles that might help to enhance stability and reduce costs in their deterrent interface. Finally, it looks at their relationship to the global non-proliferation regime, including the controversial US/India deal on nuclear energy.
A Standard Greenhouse Method for Assessing Soybean Cyst Nematode Resistance in Soybean: SCE08 (Standardized Cyst Evaluation 2008)
Authors: Niblack T. L. , Tylka Gregory L. , Arelli Prakash , Bond Jason , Diers Brian , Donald Pat , Faghihi Jamal , Gallo Karen , Heinz Robert D. , Lopez-Nicora Horacio , Von Qualen Ralph , Welacky Tom , Wilcox John 
Published: May 2009

The tactic of choice for managing soybean cyst nematode (SCN) in infested fields is the use of resistant cultivars. Because expression of SCN resistance is dependent on the occurrence and frequencies of genes for virulence in SCN populations, labeling of SCN-resistant cultivars can be difficult and, occasionally, highly misleading, leading to unanticipated yield losses. The authors' objective was to offer a set of standards for assessing and labeling SCN-resistant cultivars that would allow farmers to make direct comparisons of cultivars. Accepted for publication 15 March 2009. Published 13 May 2009.
Quantitative proteomics using formalin‐fixed paraffin‐embedded tissues of oral squamous cell carcinoma
Authors: Negishi Ayako , Masuda Mari , Ono Masaya , Honda Kazufumi , Shitashige Miki , Satow Reiko , Sakuma Tomohiro , Kuwabara Hideya , Nakanishi Yukihiro , Kanai Yae , Omura Ken , Hirohashi Setsuo , Yamada Tesshi 
Published: May 2009

Clinical proteomics using a large archive of formalin‐fixed paraffin‐embedded (FFPE) tissue blocks has long been a challenge. Recently, a method for extracting proteins from FFPE tissue in the form of tryptic peptides was developed. Here we report the application of a highly sensitive mass spectrometry (MS)‐based quantitative proteome method to a small amount of samples obtained by laser microdissection from FFPE tissues. Cancerous and adjacent normal epithelia were microdissected from FFPE tissue blocks of 10 squamous cell carcinomas of the tongue. Proteins were extracted in the form of tryptic peptides and analyzed by 2‐dimensional image‐converted analysis of liquid chromatography and mass spectrometry (2DICAL), a label‐free quantitative proteomics method developed in our laboratory. From a total of 25 018 peaks we selected 72 mass peaks whose expression differed significantly between cancer and normal tissues (P < 0.001, paired t‐test). The expression of transglutaminase 3 (TGM3) was significantly down‐regulated in cancer and correlated with loss of histological differentiation. Hypermethylation of TGM3 gene CpG islands was observed in 12 oral squamous cell carcinoma (OSCC) cell lines with reduced TGM3 expression. These results suggest that epigenetic silencing of TGM3 plays certain roles in the process of oral carcinogenesis. The method for quantitative proteomic analysis of FFPE tissue described here offers new opportunities to identify disease‐specific biomarkers and therapeutic targets using widely available archival samples with corresponding detailed pathological and clinical records. (Cancer Sci 2009; 100: 1605–1611)
[13C]‐pantoprazole breath test to predict CYP2C19 phenotype and efficacy of a proton pump inhibitor, lansoprazole
Authors: FURUTA T. , KODAIRA C. , NISHINO M. , YAMADE M. , SUGIMOTO M. , IKUMA M. , HISHIDA A. , WATANABE H. , UMEMURA K. 
Published: May 2009

SummaryBackground  13CO2 is produced on metabolism of 13C‐labelled‐pantoprazole ([13C]‐pantoprazole) by CYP2C19.Aim  To investigate whether the [13C]‐pantoprazole breath test can predict CYP2C19 status and efficacy of proton pump inhibitors (PPIs) in Japanese.Methods  We classified 110 healthy volunteers as rapid metabolizers (RM), intermediate metabolizers (IM) or poor metabolizers (PM) of CYP2C19 by genotyping. Breath samples were collected at 10‐min intervals for 60 min after dosing with 100 mg [13C]‐pantoprazole. Changes in the carbon isotope ratios (13CO2/12CO2) in carbon dioxide in breath samples were measured and expressed as a delta‐over‐baseline (DOB) ratio (‰). Of the 110 subjects, twenty‐two randomly selected subjects underwent intragastric pH monitoring on day 7 of dosing with 30 mg of lansoprazole.Results  The DOB values of RMs were the highest and those of PMs the lowest of the three groups. Statistically significant differences were observed in the area‐under‐the‐curve (AUC)20–60 min of DOB among the three groups. The mean 24‐h intragastric pHs attained by lansoprazole 30 mg for 7 days were inversely correlated with the AUC20–60 min of DOB.Conclusions  [13C]‐pantoprazole breath test can easily estimate the individual activity of CYP2C19 and predict the efficacy of a PPI (i.e. lansoprazole). This test would be useful for individualized medicine with a PPI.
Neonatal hyperthyrotropinemia: population characteristics, diagnosis, management and outcome after cessation of therapy
Authors: Zung Amnon , Tenenbaum‐Rakover Yardena , Barkan Shiri , Hanukoglu Aaron , Hershkovitz Eli , Pinhas‐Hamiel Orit , Bistritzer Tzvy , Zadik Zvi 
Published: May 2009

SummaryIntroduction  Neonatal hyperthyrotropinaemia (HT), defined by elevated TSH and normal T4, is either transient or persistent. The eventual outcome of neonatal HT is unpredictable and the management of HT patients is controversial. We assessed perinatal parameters and diagnostic measures that may distinguish between transient and persistent HT, compared with congenital hypothyroidism (CH). We also aimed to recommend optimal treatment in these forms of thyroid impairment.Design and patients  A multi‐centre, retrospective study was conducted in six paediatric endocrinology units. Forty‐three HT patients and 83 CH patients were included in the study.Measurements  We evaluated differences in birth weight (BW), gestational age (GA), modes of diagnosis, screening and confirmatory T4 and TSH levels, thyroid imaging results and optimal thyroxine doses between HT and CH and between the two forms of HT.Results  Newborns with HT had lower BW and GA than those with CH. Transient (n = 18) and persistent HT (n = 25) patients were indistinguishable by most parameters, but those with persistent HT had a higher prevalence of abnormal thyroid imaging (69%vs 8%; P = 0·005). During treatment, 79% and 55% of transient and persistent HT patients respectively experienced elevated levels of free T4. Although most HT patients were reevaluated after 2·5 years, six transient HT patients stopped therapy and showed full recovery within the first year of life.Conclusions  We recommend obtaining thyroid imaging to distinguish between the two forms of HT. Adherence to recommended doses of thyroxine and probably early cessation of therapy in transient HT can prevent iatrogenic hyperthyroidism in these patients.
Randomized study comparing endoscopic ultrasound‐guided Trucut biopsy and fine needle aspiration with high suction
Authors: Gerke H. , Rizk M. K. , Vanderheyden A. D. , Jensen C. S. 
Published: May 2009

H. Gerke, M. K. Rizk, A. D. Vanderheyden and C. S. Jensen Randomized study comparing endoscopic ultrasound‐guided Trucut biopsy and fine needle aspiration with high suctionObjectives:  Endoscopic ultrasound (EUS)‐guided Trucut biopsy (TCB) enables acquisition of tissue cores for histological assessment. Because of the rigid needle and the spring mechanism, tissue acquisition can be difficult from regions that require sharp angulation of the echoendoscope. Fine needle aspiration with high suction (FNAHS) has been proposed as a method to obtain histological tissue cores while affording the flexibility to obtain specimens even with extreme endoscope angulation. The objective was to compare prospectively these two methods in their ability to obtain specimens for histological assessment and in their diagnostic accuracy, including cytological diagnosis when achieved.Methods:  Eighty lesions in 77 patients were amenable to transoesophageal, transgastric or transrectal biopsy and were randomized to TCB (n = 44) or FNAHS (n = 36). Each specimen was assessed for adequacy (scoring system where a score of 0 was no material, 1–2 was considered cytological, and 3–5 was considered histological). Follow‐up information was obtained to establish a gold standard final diagnosis.Results:  The median histological scores for FNAHS and TCB were 2 and 5, respectively. Histological cores were obtained in 95.3% of TCB, as opposed to 27.8% in the FNAHS group (P < 0.0001). Although the diagnostic accuracy for TCB was greater than that for FNAHS (88.3% and 77.8%, respectively), this was not statistically significant (P = 0.24).Conclusion:  If histological information is required, TCB is superior to FNAHS. The difference in diagnostic accuracy did not reach statistical significance due to low numbers and the fact that FNAHS often enabled a cytological diagnosis.
Image analysis and automatic classification of transformed foci
Authors: URANI C. , STEFANINI F.M. , BUSSINELLI L. , MELCHIORETTO P. , CROSTA G.F. 
Published: May 2009

SummaryCarcinogenesis is a multi‐step process involving genetic alterations and non‐genotoxic mechanisms. The in vitro cell transformation assay allows the monitoring of the neoplastic phenotype by foci formation in suitable cells (e.g. C3H10T1/2 mouse embryo fibroblasts) showing aberrant morphology of massive build‐up, polar and multi‐layered densely stained cells. The classification of transformed foci in C3H cells relies on light microscopy scoring by a trained human expert based on standard rules. This procedure is time‐consuming and prone, in some cases, to subjectivity, thereby leading to possible over‐ or under‐estimation of the carcinogenic potential of tested compounds. Herewith we describe the in vitro neoplastic transformation induced by B[a]P and CdCl2, and the development of a foci classifier based on image analysis and statistical classification. The image analysis system, which relies on ‘spectrum enhancement’, is quantitative and extracts descriptors of foci texture and structure. The statistical classification method is based on the Random Forest algorithm. We obtained a classifier trained by using expert's supervision with a 20% classification error. The proposed method could serve as a basis to automate the in vitro cell transformation assay.
Real‐time data acquisition incorporating high‐speed software correlator for single‐molecule spectroscopy
Authors: YANG L.‐L. , LEE H.‐Y. , WANG M.‐K. , LIN X.‐Y. , HSU K.‐H. , CHANG Y.‐R. , FANN W. , WHITE J.D. 
Published: May 2009

SummarySingle‐molecule spectroscopy and detection are powerful techniques for the study of single fluorescent particles and their interaction with their environment. We present a low‐cost system for simultaneous real‐time acquisition, storage of inter‐photon arrival times and the calculation and display of the fluorescence time trace, autocorrelation function and distribution of delays histogram for single‐molecule experiments. From a hardware perspective, in addition to a multi‐core computer, only a standard low‐cost counting board is required as processing is software‐based. Software is written in a parallel programming environment with time crucial operations coded in ANSI‐C. Crucial to system performance is a simple and efficient real‐time autocorrelation algorithm (acf) optimized for the count rates (approximately 104 cps) encountered in single‐molecule experiments. The algorithm's time complexity is independent of temporal resolution, which is maintained at all time delays. The system and algorithm's performance was validated by duplicating the signal from the photon detector and sending it to both the ordinary counter board and a commercial correlator simultaneously. The data acquisition system's robustness under typical single‐molecule experimental conditions was tested by observing the diffusion of Rhodamine 6G molecules in deionized water.
Genetic differentiation and reproductive isolation of a naturally occurring floral homeotic mutant within a wild‐type population of Capsella bursa‐pastoris (Brassicaceae)
Authors: HAMEISTER STEFFEN , NEUFFER BARBARA , BLEEKER WALTER 
Published: May 2009

AbstractApart from the common floral architecture in Brassicaceae, variation in flower morphology occurs in several genera within the family and is considered to affect speciation processes. We analysed genetic differentiation and flowering time variation of two floral variants of Capsella bursa‐pastoris, the Spe variant and the wild‐type, which occur sympatrically in a vineyard in southwest Germany. The Spe variant is characterized by an additional whorl of stamens instead of petals and was formerly classified as an independent taxon ‘Capsella apetala’ Opiz. Amplified fragment length polymorphism and allozyme analysis revealed a substantial genetic differentiation of the two floral variants and a higher genetic variation within the wild‐type subpopulation compared with the Spe subpopulation. The low genetic variation in the mutant provided evidence of a recent local origin or recent introduction. Flowering time analysis indicated that, within the analysed population, the Spe variant flowers significantly later than the wild‐type (P < 0.001). We conclude that the evolution and persistence of Spe within a wild‐type population is facilitated by high selfing rates and been enhanced by a shift in flowering phenology. Hence, our data provide substantial evidence that the Spe phenotype has established itself as an isolated entity within a wild‐type population and may thus serve as a model for the analysis of the evolutionary significance of homeotic mutants in wild populations.
Dbf2 is essential for cytokinesis and correct mitotic spindle formation in Candida albicans
Authors: González‐Novo Alberto , Labrador Leticia , Pablo‐Hernando M. Evangelina , Correa‐Bordes Jaime , Sánchez Miguel , Jiménez Javier , De Aldana Carlos R. Vázquez 
Published: May 2009

SummaryWe have characterized the DBF2 gene, encoding a protein kinase of the NDR family in Candida albicans, and demonstrate that this gene is essential for cell viability. Conditional mutants were constructed by using the MET3 promoter to analyse the phenotype of cells lacking this kinase. The absence of Dbf2 resulted in cells arrested as large‐budded pairs that failed to contract the actomyosin ring, a function similar to that described for its Saccharomyces cerevisiae orthologue. In addition to its role in cytokinesis, Dbf2 regulates mitotic spindle organization and nuclear segregation as Dbf2‐depleted cells have abnormal microtubules and severe defects in nuclear migration to the daughter cell, which results in a cell cycle block during mitosis. Taken together, these results imply that Dbf2 performs several functions during exit from mitosis and cytokinesis. Consistent with a role in spindle organization, the protein localizes to the mitotic spindle during anaphase, and it interacts physically with tubulin, as indicated by immunoprecipitation experiments. Finally, DBF2 depletion also resulted in impaired true hyphal growth.
The crenarchaeal DNA damage‐inducible transcription factor B paralogue TFB3 is a general activator of transcription
Authors: Paytubi Sonia , White Malcolm F. 
Published: May 2009

SummaryTranscription initiation factor B (TFB) is conserved in eukaryotes and archaea and has an essential role in the recruitment of RNA polymerase to the promoter and the initiation of transcription. The genome of Sulfolobus solfataricus and related crenarchaea contain three paralogues of the tfb gene. Two of them (tfb1 and tfb2) encode full‐length TFB proteins. The third (tfb3) is significantly shorter than the other two, possessing an N‐terminal Zn ribbon domain but lacking the B‐finger and DNA binding domains. In S. solfataricus and Sulfolobus acidocaldarius, tfb3 is one of the most highly upregulated transcripts following exposure to UV irradiation. We demonstrate that S. solfataricus TFB3 binds to the RpoK subunit of RNA polymerase, an interaction dependent on the Zn ribbon motif of TFB3. TFB3 can also interact with the ternary complex of TBP and TFB1 bound to a DNA promoter. TFB3 stimulates transcription in vitro from several promoters in the presence of TFB1 and TBP. These observations are consistent with a model whereby TFB3 activates general transcription in trans, via an interaction with RNA polymerase in the pre‐initiation complex. This could provide a mechanism for the modulation of transcription initiation in response to environmental stresses, such as DNA damage.
Borrelia burgdorferi bb0426 encodes a 2′‐deoxyribosyltransferase that plays a central role in purine salvage
Authors: Lawrence Kevin A. , Jewett Mollie W. , Rosa Patricia A. , Gherardini Frank C. 
Published: May 2009

Summary Borrelia burgdorferi is an obligate parasite with a limited genome that severely narrows its metabolic and biosynthetic capabilities. Thus survival of this spirochaete in an arthropod vector and mammalian host requires that it can scavenge amino acids, fatty acids and nucleosides from a blood meal or various host tissues. Additionally, the utilization of ribonucleotides for DNA synthesis is further complicated by the lack of a ribonucleotide reductase for the conversion of nucleoside‐5′‐diphosphates to deoxynucleosides‐5′‐diphosphates. The data presented here demonstrate that B. burgdorferi must rely on host‐derived sources of purine bases, deoxypurines and deoxypyrimidines for the synthesis of DNA. However, if deoxyguanosine (dGuo) is limited in host tissue, the enzymatic activities of a 2′‐deoxyribosyltransferase (DRTase, encoded by bb0426), IMP dehydrogenase (GuaB) and GMP synthase (GuaA) catalyse the multistep conversion of hypoxanthine (Hyp) to dGMP for DNA synthesis. This pathway provides additional biochemical flexibility for B. burgdorferi when it colonizes and infects different host tissues.
BNR – a LINE family from Beta vulgaris– contains a RRM domain in open reading frame 1 and defines a L1 sub‐clade present in diverse plant genomes
Authors: Heitkam Tony , Schmidt Thomas 
Published: May 2009

SummaryWe characterized a novel type of plant non‐LTR retrotransposons, identified as the BNR family, in sugar beet (Beta vulgaris) genomes. Although their ORF2 sequences were similar to those of previously analysed LINEs (long interspersed nuclear elements) of the L1 clade, their ORF1 sequences differ strongly from those of most plant LINEs. Two novel domains were identified, containing a conserved secondary motif, known as the RNA recognition motif (RRM). ORF1 lacks the zinc finger motif that is typical of plant LINEs, but has an RRM that is likely to have a RNA‐binding function. BNR LINEs are highly diverse, and were characterized by gel‐blot and fluorescent in situ hybridization, showing a widespread occurrence and clustering along chromosome arms. Insertion of BNR1 into a well‐described satellite repeat was detected in two cultivars only, indicating recent activity. Database searches revealed the existence of LINE families possessing an ORF1 sequence similar to that of BNR in the genomes of higher plants such as poplar, lotus and soybean. Comparing their reverse transcriptase regions with those of other retrotransposons, these LINEs were assigned to the L1 clade, but form a distinct group, providing evidence of a major separation of L1 elements in plants. This indicates a common origin of BNR‐like LINEs, suggesting that these elements form a sub‐clade designated as the BNR sub‐clade.