bluuebunny/crossref_metadata_2025_split huggingface dataset:
STOP: searching for transcription factor motifs using gene expression
Authors: Hertzberg Libi , Izraeli Shai , Domany Eytan 
Published: May 2007

AbstractMotivation: Existing computational methods that identify transcription factor (TF) binding sites on a gene's promoter are plagued by significant inaccuracies. Binding of a TF to a particular sequence is assessed by comparing its similarity score, obtained from the TF's known position weight matrix (PWM), to a threshold. If the similarity score is above the threshold, the sequence is considered a putative binding site. Determining this threshold is a central part of the problem, for which no satisfactory biologically based solution exists.Results: We present here a method that integrates gene expression data with sequence-based scoring of TF binding sites, for determining a global score threshold for each TF. We validate our method, STOP (Searching TFs Of Promoters), in several ways: (1) we calculate the average expression values of groups of human putative target genes of each TF, and compare them to similar averages derived for random gene groups. The groups of putative targets show significantly higher relative average expression. (2) We find high consistency between the induced lists of putative targets in human and in mouse. (3) The expression patterns associated with human and mouse genes (ordered by PWM scores for each TF) exhibit high similarity between human and mouse, indicating that our method has firm biological basis. (4) Comparison of results obtained by STOP and PRIMA (Elkon et al., 2003) suggests that determining the score threshold using gene expression, as is done in STOP, is more biologically tuned.Availability: Software package will be available for academic users upon request.Contact: eytan.domany@weizmann.ac.ilSupplementary information: Supplementary data are available on Bioinformatics online.
First Report of Powdery Mildew of Eschscholzia californica (California Poppy) caused by Erysiphe cruciferarum in North America
Authors: Glawe Dean A. 
Published: May 2007

California poppy is an annual species grown widely in the Pacific Northwest. Once established, populations are self-seeding and require little care. During an ongoing study of Erysiphales, a powdery mildew fungus was collected repeatedly on this species in Seattle, WA. The fungus was determined to be Erysiphe cruciferarum Opiz ex Junell, a species not reported previously on this host in North America. This report documents the occurrence of the disease and provides information on the morphology and identification of the causal agent. Accepted for publication 8 November 2006. Published 13 December 2006.
First Report of a Serenomyces sp. From Copernicia × burretiana, Latania loddigesii, and Phoenix canariensis in Florida and the United States
Authors: Elliott M. L. , Des Jardin E. A. 
Published: May 2007

This is the first report of a Serenomyces sp. on Copernicia × burretiana, L. loddigesii, and P. canariensis in Florida and the United States. Accepted for publication 6 November 2006. Published 13 December 2006.
First Report of Powdery Mildew Caused by Golovinomyces cichoracearum on Coreopsis leavenworthii
Authors: Seijo Teresa E. , Czarnecki David , Deng Zhanao , Peres Natalia A. 
Published: May 2007

Leavenworth's tickseed (Coreopsis leavenworthii) is a native wildflower throughout Florida, and is grown commercially primarily for seed. In 2005, powdery mildew was observed on greenhouse-grown C. leavenworthii. The pathogen was identified as Golovinomyces cichorearum. This is the first report of G. cichoracearum infecting C. leavenworthii and the first report of it infecting any Coreopsis spp. in Florida. Accepted for publication 25 October 2006. Published 14 December 2006.
Bacterial Diseases of Dry Edible Beans in the Central High Plains
Authors: Harveson Robert M. , Schwartz Howard F. 
Published: May 2007

Dry beans may be affected by a number of distinct diseases, including four bacterial diseases often found occurring simultaneously in a complex. Three diseases are commonly encountered — common bacterial blight, halo blight, and bacterial brown spot — with a fourth disease (bacterial wilt) re-emerging in the Central High Plains after an absence of more than 30 years. The information in this guide may be used to identify and distinguish between the various bacterial diseases that may be encountered in dry bean production. Accepted for publication 14 October 2006. Published 25 January 2007.
Potato Yield Increases Due to Fungicide Treatment in Argentinian Early Blight (Alternaria solani) and Late Blight (Phytophthora infestans) Field Trials During the 1996-2005 Seasons
Authors: Mantecón Jorge D. 
Published: May 2007

The effect of fungicides on potato yields in separate early blight and late blight trials during the 1996 to 2005 growing seasons at the INTA Balcarce experimental station was determined. Potato cultivars Pampeana INTA were used for early blight trials while Kennebec ones were used for late blight trials. A randomized complete block design with four replications was used in all trials. The fungicides Folicur 25EC at 0.5 liter/ha and Brestan 60WP at 0.5 kg/ha were tested in early blight trials while Dithane M80WP at 2.5 kg/ha and Ridomil Gold 68WP at 1.25 kg/ha were tested in late blight trials. Early blight infections were rated using a 0 to 50 a rating scale. Late blight severity was rated using a disease index of 0 to 5. Potatoes were graded into two categories, marketable (> 60 g) and undersize tuber “seeds” (< 60 g), and then weighed. Data was subjected to analysis of variance. Early and late blight symptoms were present every season. In early blight trials, the efficacy of the systemic fungicide Folicur 25EC was greater than that of the non-systemic Brestan 60WP. The average yield increase due to fungicide treatment during the ten-year period was 22.4% for marketable and 17.9% for total yield. In late blight trials the efficacies of Dithane M80WP and Ridomil Gold 68WP were similar. The average yield increase due to fungicide treatment during the study was 41.23% for marketable and 33.85% for total yield. Accepted for publication 23 October 2006. Published 2 February 2007.
First Report of Fusarium circinatum, Causal Agent of Pitch Canker Disease, from the Roots of Mature Aleppo Pines in California
Authors: Garbelotto M. , Schweigkofler W. , Shaw D. 
Published: May 2007

A rapid decline of Aleppo pines was observed in the parking lot of the Legoland amusement park in San Diego Co., CA. Although Aleppo pine is a known host for Fusarium circinatum, this is the first report describing resin-soaked sapwood lesions in the roots of mature trees. Previous reports on root infections regarded seedlings. The infestation in this location may have begun with infected roots in planted saplings. The persistent infestation at Legoland represents a significant source of inoculum for this pathogen exotic to California. Accepted for publication 7 June 2006. Published 19 February 2007.
Potential for Soybean Cyst Nematode Reproduction on Winter Weeds and Cover Crops in Tennessee
Authors: Donald P. A. , Hayes Robert , Walker Eric 
Published: May 2007

The soybean cyst nematode (SCN), Heterodera glycines, is a major yield limiting pest of soybean (Glycine max). Current SCN management strategies include resistant soybean varieties and rotation with non-host crops. Increased adoption of the early soybean production system (ESPS) combined with a greater incidence of winter weeds from no-tillage practices may increase the population density of SCN during the noncrop period since several winter weeds and cover crops are hosts for SCN. A field experiment with a split-strip design was conducted over three years to evaluate whether SCN reproduced on weeds and cover crops during the noncrop period. Winter weeds and crimson clover roots were examined for females and cysts with eggs. The soil was sampled to determine if an increase in SCN egg population density occurred. We found no indication of SCN reproduction on winter weeds during the noncrop period or on the cover crop crimson clover. Accepted for publication 2 November 2006. Published 26 February 2007.
Desiccation at Ambient Temperature Effectively Preserves Plant Tissues Infected with Phytophthoras
Authors: Ockels Frances S. , DiLeo Matthew V. , Bonello Pierluigi 
Published: May 2007

Conventionally, plant samples collected in the course of field surveys for Phytophthora spp. (e.g., in the context of the US Forest Service-sponsored national P. ramorum survey of forest environments) are either processed immediately or stored at low temperatures and processed as soon as possible for detection by molecular methods. In order to extend the useful life of the sample, a method involving tissue desiccation was explored for effectively storing Phytophthora-infected plant leaves. In one experiment, rhododendron leaves inoculated with an unknown Phytophthora sp. and desiccated for seven days yielded DNA of sufficient quality for species identification via sequencing of the ITS region. In a second experiment, P. ramorum was successfully detected by PCR in inoculated leaves of California bay laurel, California buckeye, bigleaf maple, rhododendron, and viburnum that were desiccated and stored at room temperature for four months. Therefore, desiccation might be a viable, reliable, and less expensive alternative to storing foliar samples at low temperature. Accepted for publication 11 November 2006. Published 2 March 2007.
Phytophthora citricola Causes a Stem Canker in Black Walnut (Juglans nigra)
Authors: Beckerman Janna , Ruhl Gail 
Published: May 2007

Black walnut (Juglans nigra) is considered a premier species in the lumber industry. To our knowledge, this is the first report of Phytophthora citricola causing a stem canker on black walnut in North America. Accepted for publication 22 December 2006. Published 20 April 2007.
First Report of Melampsora euphorbiae on Poinsettia (Euphorbia pulcherrima) in Norway
Authors: Gjærum H. B. , Talgø V. , Toppe B. , Herrero M. L. , Stensvand A. 
Published: May 2007

Melampsora euphorbiae (Schub.) Cast. is reported from all continents but Antarctica. The rust fungus is living on a great number of Euphorbia species. In Norway it is found on five Euphorbia species (wild growing or cultivated outdoors), including the common weed sun spurge. To our knowledge M. euphorbiae on poinsettia has previously been reported only three times, namely in India, Tanzania, and Mauritius. Accepted for publication 16 December 2006. Published 23 April 2007.
Estimated Economic Losses Associated with the Destruction of Plants Due to Phytophthora ramorum Quarantine Efforts in Washington State
Authors: Dart Norman L. , Chastagner Gary A. 
Published: May 2007

The number and retail value of plants destroyed in Washington State nurseries due to Phytophthora ramorum quarantine efforts was estimated using Emergency Action Notification forms (EANs) issued by the United States Department of Agriculture Animal and Plant Health Inspection Service between 2004 and 2005. Data collected from EANs indicate that during this period 17,266 containerized nursery plants were destroyed at 32 nurseries, worth an estimated $423,043. The mean loss per nursery was estimated at $11,188 in 2004, $11,798 in 2005, and at $13,220 per nursery over the 2-year period. Accepted for publication 26 January 2007. Published 8 May 2007.
Lip Incompetence and Psychosocial Effects: A Pilot Study
Authors: de Oliveira Domingos Savio Ferreira , Atherino Ciriaco Cristóvão Tavares , Cervasio Marina Ribeiro , de Melo Cruz Gerarda , Cervasio Olivia Ribeiro , Bruggeman Heleen , Cornelis Liesbeth , Haspeslagh Lieve , Van Borsel John 
Published: May 2007

AbstractObjective: The purpose of the study was to determine whether children are more negatively perceived because of a lip incompetence.Study Design: A sample survey study.Methods: Two sets of colored pictures (1 set with the mouth open and 1 set with the mouth closed) were taken of four children with lip incompetence and mouth breathing and four children with normal lip closure and breathing patterns. These pictures were presented to a group of judges in Belgium and Brazil. Judges were presented either pictures of the closed mouth sets or pictures of the open mouth sets and were asked to rate on a 10‐point scale the chance that the child was shy, had few friends, belonged to a lower socioeconomic class, had problems with reading, writing, or arithmetic, had ever manifested thumb‐sucking, and had difficulties breathing through the nose. In each child, scores obtained for the open mouth set were compared with those obtained for the closed mouth set.Results: There was no consistent pattern of higher scores being assigned to the pictures of the open mouth set, neither in the Belgian survey nor in the Brazilian survey.Conclusion: Contrary with past and present claims, results suggest that children with a lip incompetence are not necessarily perceived negatively.
Partitioning the diversity of riverine fish: the roles of habitat types and non‐native species
Authors: ERőS TIBOR 
Published: May 2007

Summary1. Quantifying how biological diversity is distributed in the landscape is one of the central themes of conservation ecology. For this purpose, landscape classifications are being intensively used in conservation planning and biodiversity management, although there is still little information about their efficacy.2. I used data from 158 running water sites in Hungary to examine the contribution of six a priori established habitat types to regional level diversity of fish assemblages. Three community measures [species richness, diversity (Shannon, Simpson indices), assemblage composition] were examined at two assemblage levels (entire assemblage, the native assemblage). The relative role of non‐native species was quantified to examine their contribution to patterns in diversity in this strongly human influenced landscape.3. Additive diversity partitioning revealed the primary importance of beta diversity (i.e. among‐site factors) to patterns in species richness. Landscape‐scale patterns in species richness were best explained by between‐habitat type (beta2: 41.2%), followed by within‐habitat type (beta1: 37.7%) and finally within‐site (alpha: 21.1%) diversity. Diversity indices showed patterns different from species richness, indicating the importance of relative abundance distributions on the results. Exclusion of non‐natives from the analysis gave similar results to the entire‐assemblage level analysis.4. Canonical analysis of principal coordinates, complemented with indicator species analysis justified the separation of fish assemblages among the habitat types, although classification error was high. Multivariate dispersion, a measure of compositional beta diversity, showed significant differences among the habitat types. Contrary to species diversity (i.e. richness, diversity indices), patterns in compositional diversity were strongly influenced by the exclusion of non‐natives from the analyses.5. This study is the first to quantify how running water habitat types contribute to fish diversity at the landscape scale and how non‐native species influence this pattern. These results on riverine fish assemblages support the hypothesis that environmental variability (i.e. the diversity of habitat types) is an indication of biodiversity and can be used in large‐scale conservation designs. The study emphasises the joint application of additive diversity partitioning and multivariate statistics when exploring the contribution of landscape components to the overall biodiversity of the landscape mosaic.
Annual carbon fixation in terrestrial populations of Nostoc commune (Cyanobacteria) from an Antarctic dry valley is driven by temperature regime
Authors: NOVIS PHIL M. , WHITEHEAD DAVID , GREGORICH ED G. , HUNT JOHN E. , SPARROW ASHLEY D. , HOPKINS DAVID W. , ELBERLING BO , GREENFIELD LAURIE G. 
Published: May 2007

Abstract Nostoc commune Vaucher (a cyanobacterium) is a very conspicuous terrestrial primary producer in Victoria Land, continental Antarctica. Because polar ecosystems are considered to be especially sensitive to environmental changes, understanding the environmental constraints on net carbon (C) fixation by N. commune is necessary to determine the effects of environmental changes on the ecological functioning of ice‐free areas of the continent. A model describing net C fixation in terrestrial populations of N. commune in an Antarctic dry valley was constructed using field and laboratory measurements in which N. commune colonies were exposed to different combinations of incident irradiance (400–700 nm), temperature, and degree of desiccation. For desiccated N. commune mats with water content ≤ 30% saturation, net C fixation was highly variable between replicates and could not be modelled. However, for colonies at > 30% saturation, rates of net C fixation and dark respiration depended strongly on irradiance and temperature. Net C fixation reached a maximum rate of 21.6 μg C m− 2 s− 1 at irradiance of approximately 250 μmol m− 2 s− 1 and the optimum temperature of 20.5 °C. Agreement between predicted short‐term net C fixation and field and laboratory measurements allowed estimation of total seasonal fixation, using previously published environmental data. Annual net C fixation was estimated in the range 14.5–21.0 g C fixed m− 2Nostoc mat, depending on year/season. Estimates for different seasons correlated with thermal time (accumulated hours above 0 °C during the year) rather than irradiance, in contrast to communities in local lacustrine environments, where irradiance is the main driver of primary productivity. In the terrestrial habitat, N. commune appears to compromise between an ability to capitalize on short periods of higher temperature and efficient utilization of lower irradiance at low temperature. The relationship between thermal time and net annual C fixation by N. commune is strongly linear.
Lipopolysaccharide enhances in vivo interleukin‐2 production and proliferation by naive antigen‐specific CD4 T cells via a Toll‐like receptor 4‐dependent mechanism
Authors: Costalonga Massimo , Zell Traci 
Published: May 2007

SummaryMicrobial adjuvants are essential for the development of T‐cell‐dependent antibody production, recall T‐cell proliferation and interferon‐γ production following immunization with protein antigens. Using an adoptive transfer approach, we showed that the adjuvant lipopolysaccharide enhanced the frequency of cells producing interleukin‐2, enhanced clonal expansion by antigen‐specific CD4 T cells and increased CD86 and interleukin‐1α production by antigen‐presenting cells. All of these effects were dependent on Toll‐like receptor‐4 (TLR4) expression by cells other than the antigen‐specific CD4 T cells. The ability of lipopolysaccharides to increase the number of antigen‐specific CD4 T cells that survive after immunization probably explains the previous finding that antigen‐specific proliferation by T cells from normal mice depends on previous exposure to antigen and adjuvant.
Expression of 5‐lipoxygenase (5‐LOX) in T lymphocytes
Authors: Cook‐Moreau Jeanne M. , El‐Makhour Hojeij Yola , Barrière Guislaine , Rabinovitch‐Chable Hélène C. , Faucher Karine S. , Sturtz Franck G. , Rigaud Michel A. 
Published: May 2007

Summary5‐lipoxygenase (5‐LOX) is the key enzyme responsible for the synthesis of the biologically active leukotrienes. Its presence has been reported in cells of the myeloid lineage and B lymphocytes but has not been formally defined in T lymphocytes. In this study, we provide evidence for 5‐LOX expression on both transcriptional and translational levels in highly purified peripheral blood T cells as well as in human T lymphoblastoid cell lines (MOLT4 and Jurkat). Messenger RNA (mRNA) of 5‐LOX was amplified by conventional reverse transcription–polymerase chain reaction (RT‐PCR; MOLT4 and Jurkat cells) and by in situ RT‐PCR (T lymphocytes). 5‐LOX protein expression was confirmed by Western blot and immunofluorescence studies. 5‐LOX was present primarily in the cytoplasm with some nuclear localization and was translocated to the nuclear periphery after culture in a mitosis‐supporting medium. Fluorescence‐activated cell sorter analysis of different T‐lymphocyte populations, including CD4, CD8, CD45RO, CD45RA, T helper type 2, and T‐cell receptor‐αβ and ‐γδ expressing cells, did not identify a differential distribution of the enzyme. Purified peripheral blood T lymphocytes were incapable of synthesizing leukotrienes in the absence of exogenous arachidonic acid. Jurkat cells produced leukotriene C4 and a small amount of leukotriene B4 in response to CD3–CD28 cross‐linking. This synthesis was abolished by two inhibitors of leukotriene synthesis, MK‐886 and AA‐861. The presence of 5‐LOX in T lymphocytes but the absence of endogenous lipoxygenase metabolite production compared to Jurkat cells may constitute a fundamental difference between resting peripheral lymphocytes and leukaemic cells.
Structure of the sulfakinin cDNA and gene expression from the Mediterranean field cricket Gryllus bimaculatus
Authors: Meyering‐Vos M. , Müller A. 
Published: May 2007

AbstractThe sulfakinins are multifunctional insect neuropeptides displaying sequence similarities with the gastrin/ cholecystokinin (CCK) peptide family. In vertebrates, the peptides gastrin and CCK are involved in the regulation of digestion and food‐intake. In this study sulfakinin cDNA was cloned and sequenced from the Mediterranean field cricket Gryllus bimaculatus. The cDNA encodes two peptides flanked by endoproteolytic processing sites, designated GrybiSKI (QSDDYGHMRFG) and GrybiSKII (EPFDDYGHMRFG). The peptides include the characteristic amino acid Tyr, which is potentially sulphated, and a Gly, as a recognition site for amidation yeilding the common C‐terminal amino acid sequence of the sulfakinin peptide family. RT‐PCR studies indicate an expression of the gene restricted to the brain, with a constant level of expression throughout the last larval stage, but showing an age‐dependent decrease of expression in adult females.
Erectile dysfunction is associated with low bioactive testosterone levels and visceral adiposity in men with type 2 diabetes
Authors: Kapoor D. , Clarke S. , Channer K. S. , Jones T. H. 
Published: May 2007

SummaryLow testosterone levels in men are associated with type 2 diabetes mellitus. Erectile dysfunction (ED) is a frequent complication of type 2 diabetes. The aim of our cross‐sectional study was to investigate the relationship between ED and total, bioavailable and free testosterone levels in 198 men with type 2 diabetes. In addition, we examined the associations of various cardiovascular risk factors involved in the development of ED in type 2 diabetic men. We found that bioavailable and free testosterone levels were significantly lower in men with ED (p = 0.006 and 0.027 respectively) than those without ED. Sex hormone‐binding globulin levels were also reduced, but there was no significant difference in total testosterone (TT) levels between men with and without ED. The severity of ED as assessed by International Index of Erectile Function scores was significantly associated with TT (r = 0.32; p < 0.001), bioavailable testosterone (r = 0.32; p < 0.001) and calculated free testosterone (r = 0.35; p < 0.001) levels. ED was more frequently observed in men with hypertension and a higher waist circumference (p = 0.03). There was also a higher prevalence of ED among smokers (p = 0.06), but there were no significant associations between ED and alcohol consumption or with BMI > 30. This study has shown that ED is associated with low bioavailable and free testosterone levels, age, visceral adiposity and hypertension in type 2 diabetic men.