bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the National Plant Germplasm System's Garlic Collection for Seven Viruses
Authors: Pappu Hanu R. , Hellier Barbara C. , Dugan Frank M. 
Published: September 2008

Garlic (Allium sativum L. and A. longicuspis Regel.) germplasm maintained by the USDA-ARS Western Regional Plant Introduction Station (WRPIS) was screened for four viruses commonly infecting garlic [Garlic common latent carlavirus (GCLV), Leek yellow stripe potyvirus (LYSV), Onion yellow dwarf potyvirus (OYDV), and Shallot latent carlavirus (SLV)] plus three others [Iris yellow spot tospovirus (IYSV), Tobacco rattle tobravirus (TRV), and Tomato spotted wilt tospovirus (TSWV)]. Over 200 accessions were rated for the incidence of symptomatic plants during two production seasons, in July 2005 and June 2006. In both years, incidence of symptomatic plants ranged from less than 10% to 100% in individual accessions. Laboratory testing of selected accessions showed that the accessions were predominantly infected with OYDV (60% of infections), followed by GCLV (25%) and LYSV (15%). Accepted for publication 26 June 2008. Published 19 September 2008.
Phylogeny of embiopterans (Insecta)
Authors: Szumik Claudia , Edgerly Janice S. , Hayashi Cheryl Y. 
Published: September 2008

AbstractA cladistic analysis of embiopterans, based on 157 species (representing 70% of the known genera) and 186 morphological characters, is presented, as well as a molecular analysis for 22 taxa using genes encoding 16S, 18S and 28S rDNA and COI. Species of all known families are included, except Andesembiidae Ross (specimens of which are in a private collection). The evidence presented supports the monophyly of four of the families (Australembiidae, Oligotomidae, Teratembiidae, and Anisembiidae). Notoligotomidae is paraphyletic and included within the Afro‐neotropical family Archembiidae (which is also paraphyletic). The genera Embia, Cleomia, Macrembia, and Dihybocercus (Embiidae) form, together with Australembiidae, a group strongly supported by morphology; the position of the remaining genera of Embiidae has two quite different resolutions. Almost 80% of the genera of Anisembiidae recently described appear as either paraphyletic or polyphyletic. Contrary to the opinion of other specialists, the major groups as well as the monophyly of some families are supported by features which have been ignored in classical approaches to the systematics of Embioptera, such as the ovipositor and cephalic and leg structures, characters with an almost perfect fit.
Increased shedding of soluble fragments of P‐cadherin in nipple aspirate fluids from women with breast cancer
Authors: Mannello Ferdinando , Tonti Gaetana A. M. , Medda Virginia , Pederzoli Andrea , Sauter Edward R. 
Published: September 2008

Breast cancer, a worldwide disease with increasing incidence, develops from ductal/lobular epithelium. Nipple aspirate fluid (NAF), secreted from the breast ducts and lobules, can be analyzed to assess breast metabolic activity. P‐cadherin is frequently over‐expressed in high‐grade invasive breast carcinomas and has been reported to be an enhancer of migration and invasion of breast cancer cells, being correlated with tumor aggressiveness. The present study analyzed the soluble fragment of P‐cadherin in milk, NAF and matched plasma samples of healthy subjects and in women with precancer conditions and breast cancer. Soluble P‐cadherin was detected in all plasma and milk samples, and in about 31.3% of NAF samples. The lowest levels of soluble P‐cadherin were found in plasma, with no significant difference among NoCancer, PreCancer and Cancer patients. The highest concentration of soluble P‐cadherin was detected in milk collected during the first trimester of lactation, significantly with respect to all NAF samples. There were significantly higher levels of soluble P‐cadherin in NAF from Cancer patients than those in women with NoCancer and PreCancer (P < 0.0001). Although no significant difference was found between in situ and invasive breast cancer, soluble P‐cadherin levels were found at high concentrations in c‐erbB‐2‐positive tumors, showing a positive correlation with disease stage grouping and tumor grade, and an inverse relationship with estrogen/progesterone receptor status. High levels of the soluble fragment of P‐cadherin in Cancer NAF suggest its possible release via proteolytic processing, favoring cancer cell detachment from breast duct, and suggesting that measuring soluble P‐cadherin in NAF may improve the identification of women with increased breast cancer risk. (Cancer Sci 2008; 99: 2160–2169)
Clinical significance of pretreatment serum amphiregulin and transforming growth factor‐α, and an epidermal growth factor receptor somatic mutation in patients with advanced non‐squamous, non‐small cell lung cancer
Authors: Masago Katsuhiro , Fujita Shiro , Hatachi Yukimasa , Fukuhara Akiko , Sakuma Keiichiro , Ichikawa Masataka , Kim Yung Haku , Mio Tadashi , Mishima Michiaki 
Published: September 2008

Circulating amphiregulin and transforming growth factor‐α (TGF‐α) have been found to be correlated with an unfavorable response to gefitinib based on the identification of patients with a higher probability of resistance to the drug. However, the association between an epidermal growth factor receptor (EGFR) somatic mutation and the overexpression of its ligands has not been determined. To verify the clinical significance of the two serum markers and EGFR mutation status, we determined serum amphiregulin and TGF‐α levels by enzyme‐linked immunosorbent assay in 93 patients with advanced non‐squamous, non‐small cell lung cancer and EGFR somatic mutation status using the peptic nucleic acid‐locked nucleic acid clamp method in 46 cases. The relationship between each independent clinicopathological variable and the response to gefitinib therapy was examined. We also evaluated the risk factors associated with prognosis. Fourteen (41.0%) of 34 progressive disease cases were positive for amphiregulin (P = 0.007). Eleven (32.4%) of 34 progressive disease cases were positive for TGF‐α (P = 0.005). The median survival time of patients with the EGFR somatic mutation was significantly longer (P = 0.01). The same was true of amphiregulin‐ (P = 0.046) and TGF‐α‐negative patients (P < 0.01). In multivariate analysis, serum TGF‐α positivity (hazard ratio, 2.558; P = 0.005) and the wild type EGFR gene (hazard ratio, 1.894; P = 0.003) were significant independent prognostic factors. Our study demonstrates that the status of the serum EGFR ligand, in addition to EGFR activating mutation, is a predictive factor for response to gefitinib therapy. (Cancer Sci 2008; 99: 2295–2301)
Effects of an experimental drought and recovery on soil emissions of carbon dioxide, methane, nitrous oxide, and nitric oxide in a moist tropical forest
Authors: DAVIDSON ERIC A. , NEPSTAD DANIEL C. , ISHIDA FRANÇOISE YOKO , BRANDO PAULO M. 
Published: September 2008

AbstractChanges in precipitation in the Amazon Basin resulting from regional deforestation, global warming, and El Niño events may affect emissions of carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and nitric oxide (NO) from soils. Changes in soil emissions of radiatively important gases could have feedback implications for regional and global climate. Here, we report the final results of a 5‐year, large‐scale (1 ha) throughfall exclusion experiment, followed by 1 year of recovery with natural throughfall, conducted in a mature evergreen forest near Santarém, Brazil. The exclusion manipulation lowered annual N2O emissions in four out of five treatment years (a natural drought year being the exception), and then recovered during the first year after the drought treatment stopped. Similarly, consumption of atmospheric CH4 increased under drought treatment, except during a natural drought year, and it also recovered to pretreatment values during the first year that natural throughfall was permitted back on the plot. No treatment effect was detected for NO emissions during the first 3 treatment years, but NO emissions increased in the fourth year under the extremely dry conditions of the exclusion plot during a natural drought. Surprisingly, there was no treatment effect on soil CO2 efflux in any year. The drought treatment provoked significant tree mortality and reduced the allocation of C to stems, but allocation of C to foliage and roots were less affected. Taken together, these results suggest that the dominant effect of throughfall exclusion on soil processes during this 6‐year period was on soil aeration conditions that transiently affected CH4, N2O, and NO production and consumption.
A climatic threshold triggers the die‐off of peat mosses during an extreme heat wave
Authors: BRAGAZZA LUCA 
Published: September 2008

AbstractHeat waves, which are projected to be more frequent and intense in a warmer climate, could become a serious threat to plants that rely on water surplus availability, such as bryophytes. Here, I take the advantage of the European summer 2003 climate anomaly to assess the impact of an extreme heat wave on peat mosses of the genus Sphagnum, a group of bryophytes forming the bulk of living and dead biomass in peatlands. With this aim, 20 selected bogs in the Italian Alps were checked for Sphagnum survival in the years following the heat wave. Over the study area, the period May–September 2003 was characterized by higher mean monthly air temperature (13.5 °C) and lower mean monthly precipitation (87 mm) compared with normal climatic conditions (11.5 °C and 117 mm, respectively) so that the heat wave coincided with a drought spell. As a consequence of the unusual water stress, I documented an increased mortality of peat mosses forming high hummocks. In particular, at habitat scale, the distribution of desiccated peat mosses was restricted to the hummock face receiving the greatest amount of solar irradiation. However, at regional scale, the present study identified a climatic threshold, simply defined by the ratio of precipitation to temperature (P : T), which triggered an irreversible desiccation of peat mosses when mean monthly P : T dropped below 6.5 (mm :  °C) during May–September 2003. The absence of any sign of recovery after 4 years since the drought must be seen as a harbinger of the deleterious effects of extreme heat waves on organisms not adapted to cope with abrupt climate anomaly.
Endodontic malpractice claims in Denmark 1995–2004
Authors: Bjørndal L. , Reit C. 
Published: September 2008

AbstractAim  To study the reasons for and outcome of malpractice claims handled by the regional and national Danish Dental Complaint Boards (DCB) from 1995 to 2004. Specific attention was paid to endodontic claims. Three hypotheses were explored: endodontic malpractice claims are frequent, they are mostly due to technical shortcomings and male dentists are overrepresented.Methodology  The reasons for the claims were classified and assigned to at least one of 14 categories. Cases assigned to the ‘endodontic treatment’ category were further sub‐categorized, and reasons for malpractice were examined. An age and gender analysis of dentists and complaining patients was performed only on data obtained from the endodontic cases.Results  Overall, 3611 malpractice claims were registered. In 43% of the cases the dentist was judged to be guilty of malpractice. In the majority of the appealed cases the original verdict was affirmed (62.2%) by the national DCB. After crown & bridge treatment (23%) endodontic treatment was the next frequent malpractice claim (13.7%), in which ‘technical complications or incorrect treatment’ was the most frequent sub‐categorization (28.4%). Reasons for endodontic malpractice verdicts were related to root filling quality, the use of a paraformaldehyde product and instrument fracture. Male dentists were most often involved in an endodontic claim, and the majority of complainants were females.Conclusions  Endodontic malpractice claims were relatively common in Denmark. Perceived technical shortcomings dominated the patients′ complaints concerning root canal treatment. Male dentists and female patients were overrepresented indicating a gender influence on aspects of the doctor‐patient communication important for liability claims.
Endodontic management of badly broken down teeth using the canal projection system: two case reports
Authors: Bhomavat A. S. , Manjunatha R. K. , Rao R. N. , Kidiyoor K. H. 
Published: September 2008

AbstractAim  Teeth that have been weakened by caries and require root canal treatment to maintain their functional integrity may present with minimal coronal tooth structure and are a challenge for isolation and restoration. The aim of this clinical report is to demonstrate the management of badly broken down teeth using the Projector Endodontic Instrument Guidance System (PEIGS).Summary  The PEIGS is an adjunct to root canal treatment designed to enhance the ease of treatment delivery. Use of this system facilitates projection of canal orifices from the floor of the pulp chamber to the cavosurface, providing direct visualization of and physical access to the projected canals. This report demonstrates the use of this novel device for the management of two badly broken down teeth.Key learning points Use of the endodontic projection system has the following advantages:• ‘Projects’ the canal orifice from the floor of the pulp chamber to the cavosurface, thereby enhancing visualization and access to the canals.• The bonded coronal build up reduces the risk of interappointment crack initiation and coronal‐radicular fracture of weakened tooth structure.• Permits individualization of canals especially when they lie in close proximity to each other on the chamber floor.• Isolation may be facilitated by ease of clamp retention, rendering many structurally debilitated teeth endodontically treatable.
A Dot/Icm‐translocated ankyrin protein of Legionella pneumophila is required for intracellular proliferation within human macrophages and protozoa
Authors: Al‐Khodor Souhaila , Price Christopher T. , Habyarimana Fabien , Kalia Awdhesh , Abu Kwaik Yousef 
Published: September 2008

SummaryThe Dot/Icm type IV secretion system of Legionella pneumophila translocates numerous bacterial effectors into the host cell and is essential for bacterial proliferation within macrophages and protozoa. We have recently shown that L. pneumophila strain AA100/130b harbours 11 genes encoding eukaryotic‐like ankyrin (Ank) proteins, a family of proteins involved in various essential eukaryotic cellular processes. In contrast to most Dot/Icm‐exported substrates, which have little or no detectable role in intracellular proliferation, a mutation in ankB results in a severe growth defect in intracellular replication within human monocyte‐derived macrophages (hMDMs), U937 macrophages and Acanthamoeba polyphaga. Single cell analyses of coinfections of hMDMs have shown that the intracellular growth defect of the ankB mutant is totally rescued in cis within communal phagosomes harbouring the wild type strain. Interestingly, distinct from dot/icm structural mutants, the ankB mutant is also rescued in trans within cells harbouring the wild type strain in a different phagosome, indicating that AnkB is a trans‐acting secreted effector. Using adenylate cyclase fusions to AnkB, we show that AnkB is translocated into the host cell via the Dot/Icm secretion system in an IcmSW‐dependent manner and that the last three C‐terminal amino acid residues are essential for translocation. Distinct from the dot/icm structural mutants, the ankB mutant‐containing phagosomes exclude late endosomal and lysosomal markers and their phagosomes are remodelled by the rough endoplasmic reticulum. We show that at the postexponential phase of growth, the LetA/S and PmrA/B Two Component Systems confer a positive regulation on expression of the ankB gene, whereas RpoS, LetE and RelA suppress its expression. Our data show that the eukaryotic‐like AnkB protein is a Dot/Icm‐exported effector that plays a major role in intracellular replication of L. pneumophila within macrophages and protozoa, and its expression is temporally controlled by regulators of the postexponential phase of growth.
The rate of protein secretion dictates the temporal dynamics of flagellar gene expression
Authors: Brown Jonathon D. , Saini Supreet , Aldridge Christine , Herbert Jenny , Rao Christopher V. , Aldridge Phillip D. 
Published: September 2008

SummaryFlagellar gene expression is temporally regulated in response to the assembly state of the growing flagellum. The key mechanism for enforcing this temporal hierarchy in Salmonella enterica serovar Typhimurium is the σ28‐FlgM checkpoint, which couples the expression of the late flagellar (Pclass3) genes to the completion of the hook–basal body. This checkpoint is triggered when FlgM is secreted from the cell. In addition to the σ28‐FlgM checkpoint, a number of other regulatory mechanisms respond to the secretion of late proteins. In this work, we examined how middle (Pclass2) and late (Pclass3) gene expression is affected by late protein secretion. Dynamic analysis of flagellar gene expression identified a novel mechanism where induction of Pclass2 activity is delayed either when late protein secretion is abolished or when late protein secretion is increased. Using a number of different approaches, we were able to show that this mechanism did not involve any known flagellar regulator. Furthermore, the changes in Pclass2 activity were not correlated with the associated changes in Pclass3 activity, which was found to be proportional to late protein secretion rates. Our data indicate that both Pclass2 and Pclass3 promoters are continuously regulated in response to assembly and late protein secretion rates. These results suggest that flagellar regulation is more complex than previously thought.
Inducible protein degradation in Bacillus subtilis using heterologous peptide tags and adaptor proteins to target substrates to the protease ClpXP
Authors: Griffith Kevin L. , Grossman Alan D. 
Published: September 2008

SummaryThe ability to manipulate protein levels is useful for dissecting regulatory pathways, elucidating gene function and constructing synthetic biological circuits. We engineered an inducible protein degradation system for use in Bacillus subtilis based on Escherichia coli and Caulobacter crescentusssrA tags and SspB adaptors that deliver proteins to ClpXP for proteolysis. In this system, modified ssrA degradation tags are fused onto the 3′ end of the genes of interest. Unlike wild‐type ssrA, these modified tags require the adaptor protein SspB to target tagged proteins for proteolysis. In the absence of SspB, the tagged proteins accumulate to near physiological levels. By inducing SspB expression from a regulated promoter, the tagged substrates are rapidly delivered to the B. subtilis ClpXP protease for degradation. We used this system to degrade the reporter GFP and several native B. subtilis proteins, including, the transcription factor ComA, two sporulation kinases (KinA, KinB) and the sporulation and chromosome partitioning protein Spo0J. We also used modified E. coli and C. crescentus ssrA tags to independently control the degradation of two different proteins in the same cell. These tools will be useful for studying biological processes in B. subtilis and can potentially be modified for use in other bacteria.
Loss of cytosolic fructose‐1,6‐bisphosphatase limits photosynthetic sucrose synthesis and causes severe growth retardations in rice (Oryza sativa)
Authors: LEE SANG‐KYU , JEON JONG‐SEONG , BÖRNKE FREDERIK , VOLL LARS , CHO JUNG‐IL , GOH CHANG‐HYO , JEONG SUK‐WON , PARK YOUN‐IL , KIM SUNG JIN , CHOI SANG‐BONG , MIYAO AKIO , HIROCHIKA HIROHIKO , AN GYNHEUNG , CHO MAN‐HO , BHOO SEONG HEE , SONNEWALD UWE , HAHN TAE‐RYONG 
Published: September 2008

ABSTRACTDuring photosynthesis, triose‐phosphates (trioseP) exported from the chloroplast to the cytosol are converted to sucrose via cytosolic fructose‐1,6‐bisphosphatase (cFBPase). Expression analysis in rice suggests that OscFBP1 plays a major role in the cytosolic conversion of trioseP to sucrose in leaves during the day. The isolated OscFBP1 mutants exhibited markedly decreased photosynthetic rates and severe growth retardation with reduced chlorophyll content, which results in plant death. Analysis of primary carbon metabolites revealed both significantly reduced levels of sucrose, glucose, fructose and starch in leaves of these mutants, and a high accumulation of sucrose to starch in leaves of rice plants. In the oscfbp1 mutants, products of glycolysis and the TCA cycle were significantly increased. A partitioning experiment of 14C‐labelled photoassimilates revealed altered carbon distributions including a slight increase in the insoluble fraction representing transitory starch, a significant decrease in the neutral fraction corresponding to soluble sugars and a high accumulation of phosphorylated intermediates and carboxylic acid fractions in the oscfbp1 mutants. These results indicate that the impaired synthesis of sucrose in rice cannot be sufficiently compensated for by the transitory starch‐mediated pathways that have been found to facilitate plant growth in the equivalent Arabidopsis mutants.
Root decisions
Authors: HODGE ANGELA 
Published: September 2008

ABSTRACTRoot systems have recognizable developmental plans when grown in solution or agar; however, these plans often must be modified to cope with the prevailing conditions in the soil environment such as the avoidance of obstacles and the exploitation of nutrient‐rich patches or water zones. The modular structure of roots enables them to respond to their environment, and roots are very adaptive at modifying growth throughout the root system to concentrate their efforts in the areas that are the most profitable. Roots also form associations with microorganisms as a strategy to enhance resource capture. However, while the responses of roots in nutrient patches are well‐recognized, overall ‘rules of response’ and variation in strategy among plant species that can be applied in a number of different environments are still lacking. Finally, there is increasing evidence that root–root interactions are much more sophisticated than previously thought, and the evidence for roots to identify self from non‐self roots will be briefly discussed.
Isoprene and nitric oxide reduce damages in leaves exposed to oxidative stress
Authors: VELIKOVA VIOLETA , FARES SILVANO , LORETO FRANCESCO 
Published: September 2008

ABSTRACTIsoprene and nitric oxide (NO) are two volatile molecules that are produced in leaves. Both compounds were suggested to have an important protective role against stresses. We tested, in two isoprene‐emitting species, Populus nigra and Phragmites australis, whether: (1) NO emission outside leaves is measurable and is affected by oxidative stresses; and (2) isoprene and NO protect leaves against oxidative stresses, both singularly and in combination. The emission of NO was undetectable, and the compensation point was very low in control poplar leaves. Both emission and compensation point increased dramatically in stressed leaves. NO emission was inversely associated with stomatal conductance. More NO was emitted in leaves that were isoprene‐inhibited, and more isoprene was emitted when NO was reduced by NO scavenger c‐PTIO. Both isoprene and NO reduced oxidative damages. Isoprene‐emitting leaves which were also fumigated with NO, or treated with NO donor, showed low damage to photosynthesis, a reduced accumulation of H2O2 and a reduced membrane denaturation. We conclude that measurable amounts of NO are only produced and emitted by stressed leaves, that both isoprene and NO are effective antioxidant molecules and that an additional protection is achieved when both molecules are released.