bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields
Authors: Barutcuoglu Zafer , Airoldi Edoardo M. , Dumeaux Vanessa , Schapire Robert E. , Troyanskaya Olga G. 
Published: December 2008

AbstractMotivation: The heterogeneity of cancer cannot always be recognized by tumor morphology, but may be reflected by the underlying genetic aberrations. Array comparative genome hybridization (array-CGH) methods provide high-throughput data on genetic copy numbers, but determining the clinically relevant copy number changes remains a challenge. Conventional classification methods for linking recurrent alterations to clinical outcome ignore sequential correlations in selecting relevant features. Conversely, existing sequence classification methods can only model overall copy number instability, without regard to any particular position in the genome.Results: Here, we present the heterogeneous hidden conditional random field, a new integrated array-CGH analysis method for jointly classifying tumors, inferring copy numbers and identifying clinically relevant positions in recurrent alteration regions. By capturing the sequentiality as well as the locality of changes, our integrated model provides better noise reduction, and achieves more relevant gene retrieval and more accurate classification than existing methods. We provide an efficient L1-regularized discriminative training algorithm, which notably selects a small set of candidate genes most likely to be clinically relevant and driving the recurrent amplicons of importance. Our method thus provides unbiased starting points in deciding which genomic regions and which genes in particular to pursue for further examination. Our experiments on synthetic data and real genomic cancer prediction data show that our method is superior, both in prediction accuracy and relevant feature discovery, to existing methods. We also demonstrate that it can be used to generate novel biological hypotheses for breast cancer.Contact: ogt@cs.princeton.eduSupplementary information: Supplementary data are available at Bioinformatics online.
First Report of Bacterial Leaf Spot of Lettuce (Lactuca sativa) Caused by Xanthomonas campestris pv. vitians in Saudi Arabia
Authors: Al-Saleh M. , Ibrahim Y. 
Published: December 2008

In April of 2008, lettuce (Lactuca sativa L. cv. Darkland) plants grown in the Al-Ouunia Region of Saudi Arabia were observed with numerous lesions typical of bacterial leaf spot. Leaf lesions were irregular, small, pale green to black, and 2 to 5 mm in diameter. Bacteria were isolated from diseased leaf tissues by cutting leaves into small pieces (0.5 mm) and soaking them in 2 ml of sterile distilled water. The resulting suspension was streaked onto yeast dextrose calcium carbonate agar (YDC) (1) and plates were incubated at 28°C. Large, round, butyrus, bright yellow colonies typical of Xanthomonas spp. formed after 48 h and five strains were selected for further tests. A yellow, mucoid bacterium was consistently isolated from lettuce samples with typical bacterial leaf spot symptoms. All five strains tested in this study were gram negative, oxidase negative, nitrate reduction negative, catalase and esculin hydrolysis positive, motile, and strictly aerobic. All were slightly pectolytic but not amylolytic. All were identified as Xanthomonas campestris pv. vitians. The bacterium was identified with specific oligonucleotide primers (2). This primer pair directed the amplification of an approximately 700-bp DNA fragment from total genomic DNA of all X. campestris pv. vitians strains tested. Pathogenicity tests were performed by using bacterial cultures grown on YDC for 48 h at 28°C. Each strain was suspended in sterile distilled water and the bacterial concentration was adjusted to 106 CFU/ml. Leaves of 5-week-old lettuce plants (cv. Darkland) were sprayed with the bacterial suspension. The inoculated and sterile-water-sprayed control plants were covered with polyethylene bags for 48 h at 25°C, after which the bags were removed and plants were transferred to a greenhouse at 25 to 28°C (1). All strains were pathogenic on the lettuce cv. Darkland, causing typical bacterial leaf spot symptoms by 2 weeks after inoculation. All inoculated plants showed typical symptoms of bacterial leaf spot and symptoms similar to those observed on the samples collected. No symptoms developed on the control plants. The bacterium was reisolated from inoculated plants and identified as X. campestris pv. vitians by morphological, physiological, and biochemical tests as described above. To our knowledge, this is the first report of bacterial leaf spot of lettuce by X. campestris pv. vitians in Saudi Arabia. References: (1) F. Sahin and A. Miller. Plant Dis.81:1443, 1997. (2) J. D. Barak. Plant Dis.85:169, 2001.
First Detection of Virulence in Puccinia triticina to Resistance Genes Lr27 + Lr31 Present in Durum Wheat in Mexico
Authors: Huerta-Espino J. , Singh R. P. , Herrera-Foessel S. A. , Pérez-López J. B. , Figueroa-López P. 
Published: December 2008

Leaf rust caused by Puccinia triticina Eriks. was observed during the 2007–2008 crop season in the state of Sonora, Mexico on previously resistant durum wheat (Triticum turgidum L.) cvs. Jupare C2001 (Lr27 + 31) and Banamichi C2004. Single uredinial isolates were made from disease samples collected in the field and tested mostly on ‘Thatcher’ differentials at seedling or adult-plant stages (1). The isolates were identified as a new race, BBG/BP, resembling race BBG/BN predominant on durum wheat (2), but with additional virulences to resistance genes Lr27 + Lr31 in Gatcher and adult-plant resistance gene Lr12. The new race was also identified in samples collected from durum wheat in the State of Nuevo Leon during the same season. The avirulence/virulence formula of race BBG/BP is Lr1, 2a, 2b, 2c, 3, 3ka, 3bg, 9, 13, 14a, 15, 16, 17, 18, 19, 21, 22a, 24, 25, 26, 28, 29, 30, 32, 35, 37/Lr10, 11, 12, 14b, 20, 23, 27 + 31, 33. Although virulences to Lr27 + Lr31 and Lr12 is known to occur in P. triticina races predominant on bread wheat (T. aestivum L.) (1), to our knowledge, this is the first report of such virulences in the pathogen population on durum wheat. Pure isolates of race BBG/BP are stored in the CIMMYT leaf rust collection. References: (1) R. P. Singh. Plant Dis. 75:790, 1991. (2) R. P. Singh et al. Plant Dis. 88:703, 2004.
Phosphatidylinositol (4,5)Bisphosphate Inhibits K+-Efflux Channel Activity in NT1 Tobacco Cultured Cells
Authors: Ma Xiaohong , Shor Oded , Diminshtein Sofia , Yu Ling , Im Yang Ju , Perera Imara , Lomax Aaron , Boss Wendy F. , Moran Nava 
Published: December 2008

AbstractIn the animal world, the regulation of ion channels by phosphoinositides (PIs) has been investigated extensively, demonstrating a wide range of channels controlled by phosphatidylinositol (4,5)bisphosphate (PtdInsP2). To understand PI regulation of plant ion channels, we examined the in planta effect of PtdInsP2 on the K+-efflux channel of tobacco (Nicotiana tabacum), NtORK (outward-rectifying K channel). We applied a patch clamp in the whole-cell configuration (with fixed “cytosolic” Ca2+ concentration and pH) to protoplasts isolated from cultured tobacco cells with genetically manipulated plasma membrane levels of PtdInsP2 and cellular inositol (1,4,5)trisphosphate: “Low PIs” had depressed levels of these PIs, and “High PIs” had elevated levels relative to controls. In all of these cells, K channel activity, reflected in the net, steady-state outward K+ currents (IK), was inversely related to the plasma membrane PtdInsP2 level. Consistent with this, short-term manipulations decreasing PtdInsP2 levels in the High PIs, such as pretreatment with the phytohormone abscisic acid (25 μ m) or neutralizing the bath solution from pH 5.6 to pH 7, increased IK (i.e. NtORK activity). Moreover, increasing PtdInsP2 levels in controls or in abscisic acid-treated high-PI cells, using the specific PI-phospholipase C inhibitor U73122 (2.5–4 μ m), decreased NtORK activity. In all cases, IK decreases stemmed largely from decreased maximum attainable NtORK channel conductance and partly from shifted voltage dependence of channel gating to more positive potentials, making it more difficult to activate the channels. These results are consistent with NtORK inhibition by the negatively charged PtdInsP2 in the internal plasma membrane leaflet. Such effects are likely to underlie PI signaling in intact plant cells.
The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo
Authors: Guan X. , Silva P. , Gyenai K. B. , Xu J. , Geng T. , Tu Z. , Samuels D. C. , Smith E. J. 
Published: December 2008

SummaryThe mitochondrial genome (mtGenome) has been little studied in the turkey (Meleagris gallopavo), a species for which there is no publicly available mtGenome sequence. Here, we used PCR‐based methods with 19 pairs of primers designed from the chicken and other species to develop a complete turkey mtGenome sequence. The entire sequence (16 717 bp) of the turkey mtGenome was obtained, and it exhibited 85% similarity to the chicken mtGenome sequence. Thirteen genes and 24 RNAs (22 tRNAs and 2 rRNAs) were annotated. An mtGenome‐based phylogenetic analysis indicated that the turkey is most closely related to the chicken, Gallus gallus, and quail, Corturnix japonica. Given the importance of the mtGenome, the present work adds to the growing genomic resources needed to define the genetic mechanisms that underlie some economically significant traits in the turkey.
Evolutionarily stable oviposition and sex ratio in parasitoid wasps with single‐sex broods
Authors: CROWLEY PHILIP H. , SAEKI YORIKO , SWITZER PAUL V. 
Published: December 2008

Abstract 1. The flexibility of hymenopteran sex ratios is well documented, particularly in structured populations featuring sib mating.2. Using game theoretic models, the present study examines species producing single‐sex broods in which sib mating is unlikely, and focuses on the role of population density in determining evolutionarily stable oviposition strategies.3. Since only mated females can produce offspring of both sexes while unmated females produce only male offspring, mated females are under selection to produce more females overall to balance the primary sex ratio.4. As the proportion of all females that are mated should increase with density, offspring sex ratio of mated females is strongly linked to density at low to moderate densities. The present study shows that when density becomes low enough for fewer than half of all females to have mated, then female offspring generate higher fitness.5. In this low density situation, females may gain a fitness benefit from waiting at their emergence site or from using other costly means to find and mate with males before ovipositing.6. The predicted correspondence between females waiting at the emergence site and fewer than half of females in the population containing sperm, can be tested empirically, as can the somewhat counter‐intuitive prediction that greater access to males should yield a more male‐biased sex ratio in the offspring of mated females.7. The present study also indicates how measuring the variance in giving up times by females waiting for males at low density, can provide insight into mechanisms determining waiting times.
Nectar‐providing plants enhance the energetic state of herbivores as well as their parasitoids under field conditions
Authors: WINKLER KARIN , WÄCKERS FELIX , PINTO DELIA M. 
Published: December 2008

Abstract 1. The use of flowering vegetation has been widely advocated as a strategy for providing parasitoids and predators with nectar and pollen. However, their herbivorous hosts and prey may exploit floral food sources as well.2. Previous laboratory studies have shown that not all flower species are equally suitable in providing accessible nectar. Relatively little is known about actual nectar exploitation under field conditions.3. The present study investigates nectar exploitation by the pest, Plutella xylostella, and its parasitoid, Diadegma semiclausum, under field conditions and examines whether floral nectar exploitation in the field can be predicted based on controlled laboratory studies.4. Insects were collected from fields bordered by flowering margins containing Fagopyrum esculentum, Lobularia maritima, Anethum graveolens, Centaurea jacea or the grass Lolium perenne (control). Whole insect bodies were individually assayed by HPLC to establish their sugar profile as a measure of the level of energy reserves and the degree of food source use.5. The average overall sugar content of P. xylostella and D. semiclausum collected in fields bordered by flowering margins was significantly higher than those of individuals collected from grass‐bordered control plots. To the authors’ knowledge, this represents the first demonstration that nectar‐providing plants enhance the energetic state of herbivores under field conditions.6. In contrast to earlier laboratory studies, the present study did not find elevated sugar contents in P. xylostella and D. semiclausum individuals collected from fields bordered by buckwheat (F. esculentum).7. The present study shows widespread sugar feeding by both the herbivore and its parasitoid. It also shows that laboratory studies establishing nectar exploitation under controlled conditions can not always be extrapolated to actual exploitation under field conditions. This emphasises the importance of studying field‐collected insects with regard to food source use and nutritional status.
Electron balance during steady‐state production of CH4 and CO2 in anoxic rice soil
Authors: Yao H. , Conrad R. 
Published: December 2008

SummaryIn methanogenic rice‐field soil, organic matter (SOM) is anaerobically fermented to acetate, CO2 and H2 which then serve as substrates for methanogenesis. The whole process is a disproportionation reaction in which part of the SOM is oxidized to CO2 and part is reduced to CH4. We were interested in the electron balance during this process. The rates VCO2 and VCH4 at which CO2 and CH4 are produced by anaerobic degradation of SOM, and the fraction RH2 of the CH4 produced by reduction of CO2 with H2 (as opposed to acetotrophic methanogenesis), depend on (i) the presence or absence of inorganic oxidants and (ii) the electron balance ΔZ. Under pseudo steady‐state conditions, where inorganic oxidants are exhausted and the rate of SOM degradation is small compared with the size of the pool, VCO2, VCH4 and RH2 are constrained by ΔZ. Conversely, ΔZ may be determined from VCO2, VCH4 and RH2, all of which may be independently measured. We measured VCO2 (0.149–0.308 μmol g−1 day−1), VCH4 (0.169–0.466 μmol g−1 day−1) and RH2 (0.19–0.35) in eight soils and obtained values of ΔZ ranging from −0.918 to 0.035 μmol g−1 day−1. The majority (six) were negative, indicating a decrease in the oxidation state of the SOM carbon on degradation. This could be caused by humic acids acting as an electron acceptor and allowing more of the SOM to be oxidized to CO2 rather than reduced to CH4. Direct measurement of SOM carbon oxidation state Z produced values around zero (−0.1 ± 0.1), but is too insensitive to reveal changes of the magnitude of ΔZ.
Seasonal controls on interannual variability in carbon dioxide exchange of a near‐end‐of rotation Douglas‐fir stand in the Pacific Northwest, 1997–2006
Authors: CHEN BAOZHANG , BLACK T. ANDREW , COOPS NICHOLAS C. , KRISHNAN PRAVEENA , JASSAL RACHHPAL , BRÜMMER CHRISTIAN , NESIC ZORAN 
Published: December 2008

AbstractThis study analyzes 9 years of eddy‐covariance (EC) data carried out in a Pacific Northwest Douglas‐fir (Pseudotsuga menzesii) forest (58‐year old in 2007) on the east coast of Vancouver Island, Canada, and characterizes the seasonal and interannual variability in net ecosystem productivity (NEP), gross primary productivity (GPP), and ecosystem respiration (Re) and primary climatic controls on these fluxes. The annual values (± SD) of NEP, GPP and Re were 357 ± 51, 2124 ± 125, and 1767 ± 146 g C m−2 yr−1, respectively, with ranges of 267–410, 1592–2338, and 1642–2071 g C m−2 yr−1, respectively. Spring to early summer (March–June) accounted for more than 80% of annual NEP while late spring to early autumn (May–August) was mainly responsible for its interannual variability (∼80%). The major drivers of interannual variability in annual carbon (C) fluxes were annual and spring mean air temperatures (Ta) and water deficiency during late summer and autumn (July–October) when this Douglas‐fir forest growth was often water‐limited. Photosynthetically active radiation (Q), and the combination of Q and soil water content (θ) explained 85% and 91% of the variance of monthly GPP, respectively; and 91% and 96% of the variance of monthly Re was explained by Ta and the combination of Ta and θ, respectively. Annual net C sequestration was high during optimally warm and normal precipitation years, but low in unusually warm or severely dry years. Excluding 1998 and 1999, the 2 years strongly affected by an El Niño/La Niña cycle, annual NEP significantly decreased with increasing annual mean Ta. Annual NEP will likely decrease whereas both annual GPP and Re will likely increase if the future climate at the site follows a trend similar to that of the past 40 years.
Fluorescence combined with excised patch: measuring calcium currents in plant cation channels
Authors: Gradogna Antonella , Scholz‐Starke Joachim , Gutla Paul Vijay Kanth , Carpaneto Armando 
Published: December 2008

SummaryCombined application of the patch–clamp technique and fura‐2 fluorescence detection enables the study of study calcium fluxes or related increases in cytosolic calcium concentration. Here we used the excised patch configuration, focusing the photomultiplier on the tip of the recording pipette where the fluorescent dye was present (FLEP, fluorescence combined with excised patch). This configuration has several advantages, i.e. a lack of delay in loading the fluorophore, of interference by internal calcium buffers and of photobleaching, due to the quasi‐infinite dye reservoir inside the pipette. Upon voltage stimulation of tonoplast patches, sustained and robust fluorescence signals indicated permeation of calcium through the slow vacuolar (SV) channel. Both SV currents and fluorescence signal changes were absent in the presence of SV channel inhibitors and in vacuoles from Arabidopsis tpc1 knockout plants that lack SV channel activity. The fractional calcium currents of this non‐selective cation channel were voltage‐dependent, and were approximately 10% of the total SV currents at elevated positive potentials. Interestingly, calcium permeation could be recorded as the same time as oppositely directed potassium fluxes. These events would have been impossible to detect using patch–clamp measurements alone. Thus, we propose use of the FLEP technique for the study of divalent ion‐selective channels or transporters that may be difficult to access using conventional electrophysiological approaches.
An approach for post‐market monitoring of potential environmental effects of Bt‐maize expressing Cry1Ab on natural enemies
Authors: Sanvido O. , Romeis J. , Bigler F. 
Published: December 2008

AbstractPost‐market monitoring (PMM) consistent with Swiss and European Union legislation should ensure the detection and prevention of adverse effects on the environment possibly deriving from commercial cultivation of genetically modified (GM) crops. Insect‐resistant GM crops (such as Bt‐maize) raise particular questions regarding disturbances of biological control functions provided by beneficial insects such as predators and parasitoids (so‐called natural enemies). Consensus among regulators, scientists and the agricultural biotech industry on appropriate PMM plans allowing the detection and possibly prevention of such adverse effects is still lacking. The aims of this study were to identify the necessity for PMM of Bt‐maize expressing Cry1Ab on natural enemies and to develop an appropriate PMM plan. The approach chosen consisted in determining what type of monitoring is most appropriate to address potential effects of Bt‐maize on natural enemies during commercial cultivation. This included identifying whether there remain substantial scientific uncertainties that would support case‐specific monitoring. Existing pre‐market risk assessment data indicate that Bt‐maize (Cry1Ab) comprises a negligible risk for disturbances in biological control functions of natural enemies. As a consequence, a faunistic monitoring of specific groups of natural enemies is not considered an appropriate approach to detect failures in biological control functions. Alternatively, an approach is proposed that consists in indirectly analysing biological control functions by surveying outbreaks of maize herbivores. Unusual herbivore outbreaks could indicate failures in biological control functions of natural enemies. Data could be collected via questionnaires addressed to farmers growing Bt‐maize. Significant correlations between unusual occurrences of specific maize herbivores and the cultivation of Bt‐maize would subsequently need specific studies to determine possible causalities in more detail. The here proposed approach has the advantage of covering different natural enemy groups. It represents a cost‐effective strategy to obtain scientifically sound data as a basis for regulatory decision‐making.
CHYLURIA
Authors: Lloyd‐Davies R. W. , Edwards J. M. , Kinmonth J. B. 
Published: December 2008

SUMMARYThe clinical features of chyluria have been described and the ztiology, pathology and treatment reviewed and illustrated by case reports.The commonest ætiological agent remains filariasis. Chylous reflux due to incompetent megalymphatics and primary lymphatic disease is an established but rare cause.The importance of full investigation is stressed, especially that of pedal lymphangiography. By combination with pyelography, the site of the fistula may be demonstrated.Direct surgical approach to the communicating lymphatics is effective, and is now the treatment of choice.
Changes in dipole membrane potential at the mouse blood–brain barrier enhance the transport of99mTechnetium Sestamibi more than inhibiting Abcb1, Abcc1, or Abcg2
Authors: Cattelotte Julie , Tournier Nicolas , Rizzo‐Padoin Nathalie , Schinkel Alfred H. , Scherrmann Jean‐Michel , Cisternino Salvatore 
Published: December 2008

AbstractCationic99mTc‐agents like99mTc‐hexakis‐2‐methoxyisobutyl isonitrile (99mTc‐MIBI) cannot be used for brain imaging because they do not enter the brain as readily as some uncharged99mTc‐compounds. The mechanism by which cationic99mTc‐agents are transported across the blood–brain barrier (BBB) remains unclear. We explored99mTc‐MIBI transport byin situmouse brain perfusion to determine the influence of BBB features like the ATP‐binding cassette transporters (Abcb1/P‐glycoprotein (P‐gp), Abcc1/Mrp1, and Abcg2/Bcrp), organic cation transporters (Slc22a1‐3/Oct1‐3), the transmembrane potential and the dipole membrane potential. P‐gp reduced99mTc‐MIBI transport across the BBB of P‐gp‐deficient mice 2.2‐fold, as confirmed by PSC833 and GF120918 inhibition. Paradoxically verapamil decreased its transport ‘0.6‐fold’. Reducing the BBB dipole membrane potential with tetraphenylborate or phloretin increased99mTc‐MIBI transport about 12‐ and 20‐fold, respectively. Guanidine, diphenhydramine, and carnitine significantly decreased99mTc‐MIBI transport, but tetraethylammonium did not.99mTc‐MIBI transport at the BBB is restricted by P‐gp but not by Mrp1 or Bcrp. Some organic cations reduced the influx of99mTc‐MIBI into the brain independently of Oct1, 2 and 3, but this could be due to their effect on another cation transporter. The membrane dipole potential of the luminal BBB membrane appeared to be the main factor restricting99mTc‐MIBI permeability.