bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of institutions on the decision how to decide
Authors: ENGEL CHRISTOPH , WEBER ELKE U. 
Published: October 2007

Abstract:Institutions influence and shape behaviour. This paper suggests one way in which they do so that has been largely overlooked in institutional analysis and design. When faced with a decision or problem, people have more than one mechanism at their disposition for addressing it. The human mind offers multiple tools, ranging from conscious deliberation to spontaneous, affective reactions. Relying on technology or experts, decision-makers can also muster additional resources. Often, the meta-choice of which decision-making or problem-solving mode is used has an impact on the output. Some normative goals are more likely met if the decision-maker uses a specific problem-solving mode. We argue that the meta-choice of which problem-solving mode to use for a given decision can be influenced by institutions. In the interest of defining access points for institutions, we develop a conceptual framework for the selection and implementation of decision-making and problem-solving modes.
Naturalizing the market on the road to revisionism: Bruce Caldwell'sHayek's challengeand the challenge of Hayek interpretation
Authors: MIROWSKI PHILIP 
Published: October 2007

Abstract:Bruce Caldwell'sHayek's Challengeshould be welcomed as the first serious book on one of the most important thinkers of the twentieth century. However, this review begins by pointing out a number of curious omissions and silences concerning Hayek's career in the book. We propose that the key to understanding the turns and reversals in his thought lay in his politics, and not as Caldwell has it, in some abstract philosophical doctrines. Central to that thesis is Hayek's fostering the development of Neoliberalism through such institutional structures as the Mont Pèlerin Society.
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics
Authors: Smith Andrew , Cheung Kei , Krauthammer Michael , Schultz Martin , Gerstein Mark 
Published: October 2007

AbstractMotivation: Proteomics researchers need to be able to quickly retrieve relevant information from the web and the biomedical literature. To improve information retrieval, we leverage the structure of the semantic web, developing an approach for joining it with the largely opposing paradigm of unsupervised web search.Results: Our approach uses a Resource-Description-Framework (RDF) graph that inter-relates documents through their associated biological identifiers (e.g., protein ID). A search begins with a simple query term (UniProt identifier), which is expanded with terms extracted from documents in the RDF graph surrounding the query (“the subgraph”). We re-rank documents in the full corpus (e.g. all PubMed) by their cosine-similarity scores against a composite word-weight vector created from the subgraph. This vector is a weighted sum of individual word-weight vectors for documents at each node of the subgraph, taking into account the types of relationships between the central query identifier and the nodes connected to it. The computation also uses inverse document frequency (IDF) in a novel way to rescale the local word frequencies in the query's subgraph relative to that in other subgraphs. Applying our procedure to PubMed, we optimize weights for various relationships in the subgraph and benchmark overall performance in detail. Using a subgraph containing family relationships (from PFAM) results in a significant improvement in accuracy (as compared to not considering the subgraph in the search) when assessed against known relationships in the yeast literature. Moreover, we achieve this accuracy using only relatively simple and computationally efficient methods.Contact: mark.gerstein@yale.eduSupplementary information: http://hub.gersteinlab.org/ir-supp/
Impatiens necrotic spot virus and Tomato spotted wilt virus Diagnosed in Phalaenopsis Orchids from Two Florida Nurseries
Authors: Baker C. A. , Davison D. , Jones L. 
Published: October 2007

In October 2006 (Arcadia, FL) and January 2007 (Sorrento, FL), several white Phalaenopsis orchids with large chlorotic/necrotic ringspot symptoms were sent to the Division of Plant Industry, Gainesville, FL. Symptomatic leaf tissues were tested with the Agdia immunostick-comb (Agdia, Elkhart, IN) for Impatiens necrotic spot virus (INSV), Tomato spotted wilt virus (TSWV), Cucumber mosaic, and Tobacco mosaic virus. Plants from the nursery in Sorrento, FL tested positive for TSWV, while those from the nursery in Arcadia, FL tested positive for INSV. Symptomless leaves from the infected plants tested negative for the viruses with the immunostick-comb. The plants also were tested for TSWV and INSV by double-antibody (DAS)-ELISA (Agdia Inc.) with the same results. Total RNA was extracted from one symptomatic orchid leaf from each nursery. Reverse transcription (RT)-PCR was performed with the universal tospovirus primer set BR60and BR65 (1). PCR bands of the expected size were amplified from each leaf. PCR products were sequenced directly. The orchid leaf that tested positive for TSWV by ELISA produced a 495-bp sequence with 97% identity to several isolates of the TSWV nucleocapsid protein gene listed in GenBank (Accession Nos. AY744479, AY8770391, DQ376185, and AF02659). The orchid leaf that tested positive for INSV by ELISA produced a 396-bp sequence with 98 to 99% identity to several isolates of the INSV nucleocapsid protein gene (Accession Nos. D00914, DQ425096, X66972, and AD109100). Although these viruses have been reported a few times in orchids previously (2,3), to our knowledge, this is the first time they have been reported in this host in Florida. In addition, white Phalaenopsis spp. appears to be a local lesion host and not a systemic host for these viruses. References: (1) M. Eiras et al. Fitopatol. Bras. 26:170, 2001. (2) J. S. Hu et al. Plant Dis. 77:464, 1993. (3) S. T. Koike and D. E. Mayhew. Orchids 70:746, 2001.
First Report of Leaf Spot and Root Rot Caused by Phoma betae on Beta vulgaris subsp. vulgaris (Garden Beet Group) in Italy
Authors: Garibaldi A. , Gilardi G. , Bertetti D. , Gullino M. L. 
Published: October 2007

In the winter of 2007 in Piedmont (northern Italy), symptoms of a previously unknown disease were observed on beet (Beta vulgaris L. subsp. vulgaris) (garden beet group) grown under a tunnel on several commercial farms near Cuneo. First symptoms appeared on 1-month-old plants, occurring as brown, round-to-oval spots as much as 2 cm in diameter with dark concentric rings near the perimeter. Small, dark pycnidia were present throughout the spots in concentric rings. Generally, older, lower leaves were affected more than the younger ones. Ten to fifteen percent of the plants were affected. Symptoms on the roots began near the crown as small, dark, sunken spots that became soft and water soaked. Eventually, spots on the roots turned dark brown to black and black lines separated diseased and healthy tissues. Older infected tissues were black, dry, shrunken, and spongy. Pycnidia were not observed on affected roots. From infected leaves and roots, a fungus was consistently isolated on potato dextrose agar (PDA) amended with 25 mg/l of streptomycin. The fungus was grown on PDA and maintained at 22°C (12 h of light, 12 h of dark). After 10 days, black pycnidia (130 to 328 [204] μm in diameter) developed, releasing abundant hyaline, elliptical, nonseptate conidia measuring 3.9 to 6.7 (5.1) × 2.4 to 5.9 (3.6) μm. On the basis of its morphological characteristics, the fungus was identified as a Phoma sp. (1). The internal transcribed spacer (ITS) region was amplified using primers ITS4/ITS6 (2) and sequenced. BLASTn analysis of the 557 bp obtained showed an E-value of 0.0 with Phoma betae. The nucleotide sequence has been assigned GenBank Accession No. EU003450. Pathogenicity tests were performed by spraying leaves of healthy 20-day-old potted B. vulgaris plants with a spore and mycelial suspension (1 × 106 spores or mycelial fragments per ml). Noninoculated plants sprayed only with water served as controls. Fifteen plants (three per pot) were used for each treatment. Plants were covered with plastic bags for 5 days after inoculation and kept in a growth chamber at 20°C. Symptoms previously described developed on leaves of all inoculated plants 5 days after inoculation, while control plants remained healthy. Later, pycnidia and conidia, with the same dimensions and characteristics previously described, were observed on the infected leaves. The fungus was consistently reisolated from the lesions of the inoculated plants. The pathogenicity test was carried out twice. P. betae on B. vulgaris var. cycla has been reported in Canada (3) as well as in other countries. The same pathogen was reported in Italy on sugar beet (2). References: (1) G. H. Boerema and G. J. Bollen. Persoonia 8:111, 1975. (2) A. Canova. Inf. Fitopatol. 16:207, 1966. (3) D. E L. Cooke and J. M. Duncan. Mycol. Res. 101:667, 1997. (4) J. R. Howard et al. Diseases of Vegetable Crops in Canada. Canadian Phytopathological Society, 1994.
First Report of Cucumber mosaic virus in Echium candicans in France
Authors: Cardin L. , Moury B. 
Published: October 2007

Echium candicans (Linn.) Herb. Banks (Pride of Madeira or Viper's Bugloss), family Boraginaceae, is a perennial shrub used in gardens for the ornamental quality of its deep blue inflorescences, especially in coastal areas near the Mediterranean Sea. Mosaic symptoms were observed in leaves of E. candicans in the Alpes Maritimes Department of southeastern France, St Jean Cap Ferrat in 1994, Menton in 2002, and Antibes in 2005. Symptoms exhibited in a range of inoculated plants including Nicotiana tabacum cvs. Xanthi and Samsun, Chenopodium quinoa, C. amaranticolor, Vigna unguiculata cv. Black, and Cucumis sativus cv. Poinsett were typical of Cucumber mosaic virus (CMV). Occurrence of CMV in one sample from each of the three localities was confirmed by the observation of isometric particles (approximately 30 nm) with the electron microscope in crude sap preparations from the infected plants, positive reactions in double-antibody sandwich (DAS)-ELISA to polyclonal antibodies raised against CMV (1), and the nonpersistent transmission of the virus from infected Xanthi to virus-free Xanthi plants by Myzus persicae. In double-immunodiffusion analysis, the three isolates were shown to belong to the CMV subgroup II (1,2). To determine if CMV was responsible for the symptoms observed, the isolate from Antibes was multiplied in Xanthi plants after isolation from local lesions on V. unguiculata and mechanically inoculated to 3-year-old plants of E. candicans tested to be free from CMV before the mechanical inoculation. One month after inoculation, mild mosaic symptoms were observed in young leaves and CMV was detected by DAS-ELISA in 10 of 10 inoculated plants. To our knowledge, this is the first report of CMV in E. candicans. References: (1) J.-C. Devergne and L. Cardin. Ann. Phytopathol. 7:225, 1975. (2) M. J. Roossinck. J. Virol. 76:3382, 2002.
Momordica charantia is a Weed Host Reservoir for Papaya ringspot virus Type P in Jamaica
Authors: Chin M. , Ahmad M. H. , Tennant P. 
Published: October 2007

Papaya rinsgpot virus type P (PRSV), a member of the genus Potyvirus in the family Potyviridae, is primarily transmitted by aphids in a nonpersistent manner (2). The virus is geographically widespread but has a narrow host range within the plant families Caricaceae, Chenopodiaceae, and Cucurbitaceae (2). The first reported epidemic of PRSV in Jamaica was during the late 1980s (1). Since then, the virus has spread across the island and is recognized as a potential problem for continued production of papaya (Carica papaya L.). In the summers of 1999 and 2000, prominent vein clearing symptoms were observed on leaves of a common weed, cerasee (Momordica charantia L.), in papaya orchards of western Jamaica. This weed, a climbing annual in the Cucurbitaceae family used in a variety of local herbal preparations, was found to be growing on fences or the ground along the periphery of the orchards. Leaf samples were collected and tested for PRSV by double-antibody sandwich (DAS)-ELISA with polyclonal antibodies (Agdia Inc, Elkhart, IN). In addition, crude sap extracts from 12 cerasee leaf samples that were diluted 1:20 were mechanically inoculated onto six plants each of cerasee and papaya. Within 2 weeks, vein clearing symptoms were observed on cerasee and symptoms (vein clearing followed by mosaic development and leaf distortions) typical of PRSV infection were obtained on papaya (2). All original leaf samples and inoculated plants tested positive in DAS-ELISA. In subsequent vector transmission tests, 10 healthy cerasee or papaya seedlings were inoculated with aphids (Aphis gossypii) that were previously permitted to feed on PRSV-infected papaya or cerasee. High rates of virus transmission were achieved in three tests from cerasee to papaya (77 to 83%), papaya to cerasee (90 to 93%), and cerasee to cerasee (60 to 70%). Total RNA from papaya samples was subjected to reverse transcriptase-PCR using primers to the capsid protein gene (3). A single fragment of the expected size (approximately 996 bp) was amplified and sequenced and showed high nucleotide identity (90.3 to 91.4%) with previously reported PRSV type P from Jamaica (GenBank Accession No. DQ104823), Cuba (GenBank Accession No. DQ089482), Florida (GenBank Accession No. AF196839), Brazil (GenBank Accession No. AF344650), and Hawaii (GenBank Accession No. S46722). To our knowledge, this is the first report of the natural occurrence of PRSV on a weed host in Jamaica. Because of its widespread distribution and potential of serving as a reservoir of PRSV, cerasee may play a role in the epidemiology of PRSV. References: (1) M. Chin et al. Jam. J. Sci. Technol. 14:58, 2003. (2) D. Purcifull et al. No 292 in: Descriptions of Plant Viruses. CMI/AAB, Surrey, England, 1984. (3) J. Slightom. Gene 100:251, 1991.
Recovery and collapse of the Far Eastern sardine
Authors: KAWASAKI T. 
Published: October 2007

ABSTRACTThe Far Eastern sardine (Sardinops sagax) began to increase dramatically in the early 1970s, reached a peak in the late 1980s, but then decreased thereafter. This dramatic recovery and collapse is the second cycle this century, and constitutes part of a long‐term structural change in a pelagic fish community. The new cycle was initiated with higher survival at the earliest stages of sardine on both coasts of central Japan and they spread to the north, south and offshore. Strong year classes were produced at short intervals. The spawning area moved westward and inshore. Collapse was caused by survival failure. The spawning activity shifted to theeast and offshore and the range of the sardine was reduced. Recovery was triggered by global climatic change in a density‐independent manner and the collapse underway is caused by a density‐dependent mechanism. The sardine is the keystone species in the pelagic fish community and changes of mackerel (Scomber japonicus) and anchovy (Engraulis japonicus) populations are in progress.
Loss of myoepithelium is variable in solid papillary carcinoma of the breast
Authors: Nicolas M M , Wu Y , Middleton L P , Gilcrease M Z 
Published: October 2007

Aims:  Reports on the frequency of myoepithelial loss in solid papillary carcinoma (SPC) of the breast, an unusual variant of papillary carcinoma with a solid pattern of expansile growth, have been strikingly contradictory. The aim was to clarify the frequency of myoepithelial loss in cases of SPC diagnosed at our institution.Methods and results:  Eleven cases of SPC with available blocks or unstained slides were retrieved from the M. D. Anderson archives or obtained from outside contributors. Immunohistochemistry for smooth muscle actin (SMA) and p63 was evaluated on the circumscribed nests that appeared to be non‐invasive by haematoxylin and eosin morphology. Three of the 11 cases (27%) were positive for both SMA and p63 at the periphery of all such foci, whereas eight cases (73%) lacked staining for both myoepithelial markers in at least one focus. Of these eight cases, one was diagnosed with only microinvasion, yet metastatic tumour resembling the circumscribed primary SPC was identified in two ipsilateral axillary lymph nodes.Conclusions:  SPC of the breast frequently lacks myoepithelial markers at the tumour–stromal interface in spite of a circumscribed non‐invasive appearance. Metastases from such tumours are infrequent, but can occur in cases that lack myoepithelial marker expression by immunohistochemistry.
Gastric and intestinal diffuse large B‐cell lymphomas are clinically and immunophenotypically different. An immunohistochemical and clinical study
Authors: Connor J , Ashton‐Key M 
Published: October 2007

Aims:  To determine the immunophenotype of gastric and intestinal diffuse large B‐cell lymphomas and investigate the clinical significance of patterns of antigen expression.Methods and results:  Immunohistochemistry was performed for detection of CD10, Bcl‐6, Bcl‐2, MUM1 and p53 in paraffin‐embedded tissue from 29 patients with primary diffuse large B‐cell lymphoma of the stomach and intestine. Statistical analysis was performed using χ2 and Fisher’s exact tests. Survival data were analysed by the Kaplan–Meier method and compared using a log rank test. Thirteen of the 29 cases were of germinal centre phenotype (CD10+ or CD10–, Bcl‐6+ and MUM1–). Sixteen were of activated B‐cell phenotype (all CD10– and either Bcl‐6–, or Bcl‐6+ and MUM1+). Sixteen cases showed Bcl‐2 expression. There was a statistically significant difference (P < 0.05) in immunophenotype of the neoplastic cells relating to tumour site. Of 15 gastric lymphomas, 11 were of activated B‐cell phenotype and 9/14 intestinal tumours were of germinal centre phenotype. No significant survival difference was found between groups with regard to expression of any of the antigens investigated.Conclusions:  Primary gastric and intestinal large cell lymphomas appear to show different patterns of antigen expression. This suggests that these tumours arise by different mechanisms and/or from different causes. Gastric diffuse large B‐cell lymphomas are usually of activated B‐cell phenotype that may reflect a relationship with low‐grade gastric lymphomas of marginal zone type. Intestinal diffuse large B‐cell lymphomas usually show a germinal centre phenotype, suggesting an origin from germinal centre B cells. In this study the tumour immunophenotype was not associated with any difference in survival.
Differential suppression of experimental allergic diseases in rats infected with trypanosomes
Authors: MACKENZIE A.R. , SIBLEY P.R. , WHITE B.P. 
Published: October 2007

Summary PVG/c rats, infected 3 days previously with 103 Trypanosoma brucei brucei S.42 organisms failed to develop adjuvant disease in response to an intradermal inoculation of mycobacterial adjuvant. By contrast, similarly infected rats, immunized with heterologous brain and spinal cord in Freund's complete adjuvant with pertussis vaccine as a secondary adjuvant, developed clinical signs of allergic encephalomyelitis (EAE) at least as severe as those in uninfected rats.Delayed hypersensitivity reactions to PPD were depressed in trypanosome‐infected, adjuvant‐injected rats, as were the reactions to myelin basic protein in infected rats developing EAE. There appeared to be no cross‐reactivity between trypanosomal antigen and myelin basic protein which could account for the lack of suppression of EAE.It is suggested that the different extent to which autoimmunity is involved in these two experimental allergic diseases may account for the differential suppressive activity of trypanosome infections upon them.
Schistosoma mansoni: age‐dependent susceptibility to immune elimination of schistosomula artificially introduced into preinfected mice
Authors: BLUM K. , CIOLI D. 
Published: October 2007

SUMMARYMice chronically infected with Schistosoma mansoni exhibited a significant resistance to a second infection with the same parasite, as demonstrated by their challenge worm burdens measured by portal perfusion. A decreased worm recovery was also exhibited by chronically infected mice when the challenge was administered intravenously using 3‐h schistosomula obtained by the isolated skin technique or using 5‐, 6‐, 7‐ and 9‐day‐old schistosomula obtained from the lungs ofinfected donor mice. Variable results were obtained with 10‐ and II‐day‐old forms, while schistosomula which were 12days old or older, did not undergo significant rejection when introduced into the mesenteric veins of preinfected mice. Attempts to analyse these phenomena using the‘lung assay’were made complicated by the observation that the day of maximum recovery from the lungs was dependent upon the age of injected worms.
The response of mice immune to Schistosoma mansoni to a challenge infection which bypasses the skin: evidence for two mechanisms of immunity
Authors: MILLER K.L. , SMITHERS S. R. , SHER A. 
Published: October 2007

SUMMARYMice which had developed immunity to reinfection with Schistosoma mansoni following exposure to 20 cercariae and mice which had been immunized against S. mansoni by exposure to 400 highly irradiated (20 krad) cercariae, were tested for their ability to resist a percutaneous cercarial challenge and an intravenous challenge with 5‐day‐old lung‐stage schistosomula derived from the same cercariae. Although both types of immune mice showed a marked resistance to a cercarial challenge, only the infected mice showed a comparable immunity to an intravenous challenge with lung schistosomula. These results confirm earlier studies which suggest that the major attrition of a cercarial challenge in infected mice occurs at the post‐lung stage, whilst the attrition of a challenge infection in mice immunized with highly irradiated cercariae takes place in the skin. They provide further evidence for two separate mechanisms of immunity against S. mansoni in mice.
Serum‐mediated adherence of feline granulocytes to microfilariae of Brugia pahangi in vitro: variations with parasite maturation
Authors: JOHNSON P. , SUSWILLO R.R. , DENHAM D.A. 
Published: October 2007

SUMMARYFeline eosinophils and neutrophils readily adhered in vitro to the sheaths of microfilariae of Brugia pahangi in the presence of suitable serum. Both cell types flattened along the surface of the parasite undergoing cytoplasmic changes which included degranulation. Adherence was dependent on properties of both the serum and the history of the microfilaria used. Two types of serum factor were found to mediate adherence. Heat labile factors were present in sera from infected and uninfected cats as well as in sera from other species. They were removed by preincubation of sera with zymosan suggesting that complement components were involved. This suggestion was supported by the demonstratior, of C3 on the surface of microfilariae participating in adherence reactions. A heat stable factor, present in the serum of less than 10% of infected cats, also mediated adherence. This factor was demonstrated to be IgG by immunoadsorption and immunofluorescence. The ability of the microfilariae to participate in the adherence reaction mediated by complement factor varied with maturation of the parasite. Microfilariae obtained directly from the uteri of adult worms, or produced in vitro, did not possess the ability to participate in adherence. Young blood microfilariae (i.e. taken from the blood of cats recently patent) were similar to the in vitro produced parasites; however, the majority of blood microfilariae from infections of greater than three weeks patency participated in this form of adherence. No difference between blood and uterinelin vitro microfilariae was seen in adherence reactions mediated by heat stable antibody.