bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Spruce Needle Drop Associated with Setomelanomma holmii on Spruce in Illinois
Authors: Plewa D. E. , Jossey S. , Porter S. K. , Bissonnette S. M. 
Published: November 2011

Spruce needle drop (also known as sudden needle drop of spruce, both referred to as SNEED) is a condition consistently associated with the fungus Setomelanomma holmii. While the pathogenicity of this fungus is still under investigation, it has been reported to cause the discoloration and needle drop of older needles on white spruce (Picea glauca) and Colorado blue spruce (P. pungens) (1). In the spring and summer of 2011, the University of Illinois Plant Clinic received several samples of Norway spruce (P. abies) and Colorado blue spruce branches that all exhibited the same symptoms: browning of older needles followed by needle drop. Solitary, black, globose, 105 to 230 μm diameter pseudothecia were observed on the upper surface of the branches and bud scales with a dissecting microscope. Many of the fruiting structures contained setae. When examined under a compound microscope, asci were bitunicate, 60 to 100 × 10.5 to 15 μm (mean 71.9 × 12.7 μm), and contained eight pale brown, three-septate, 15.5 to 22.5 × 5.5 to 9 μm (mean 19.4 × 5 μm) ascospores. On the basis of the asci and ascospores, the fungus was tentatively identified as S. holmii. To confirm the identification, single-ascospore colonies were cultured on acid potato dextrose agar. DNA was extracted from the mycelia of a single colony and amplified with PCR using universal fungal primers (2). The amplified DNA was sequenced and assembled using the primers NS1, NS3, NS5, and NS7 in the forward direction and NS2, NS4, NS6, and NS8 in the reverse direction (2). When the consensus sequence was compared with all accessions in the National Center for Biotechnology Information GenBank nucleotide collection, it had 100% homology to the S. holmii 18S ribosomal gene (Accession No. AY161121, isolated from a sample of P. pungens collected in France). S. holmii was first observed in the United States in 1998 (1). Although it has been tentatively identified on the basis of morphological characteristics in many states in the Midwest, this is the first time it has been conclusively identified in Illinois to our knowledge. Additionally, this is the first time Norway spruce has been confirmed as a host of S. holmii based on genetic sequencing in Illinois. Sporulation has been observed from mid-May through early August. Currently, the presence of S. holmii has been confirmed in 14 counties in central and northern Illinois. References: (1) A. Rossman et al. Can. J. Bot. 80:1209, 2002. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al. eds. Academic Press, San Diego, CA, 1990.
A computable evolution equation for the joint response-excitation probability density function of stochastic dynamical systems
Authors: Venturi D. , Sapsis T. P. , Cho H. , Karniadakis G. E. 
Published: November 2011

By using functional integral methods, we determine a computable evolution equation for the joint response-excitation probability density function of a stochastic dynamical system driven by coloured noise. This equation can be represented in terms of a superimposition of differential constraints, i.e. partial differential equations involving unusual limit partial derivatives, the first one of which was originally proposed by Sapsis & Athanassoulis. A connection with the classical response approach is established in the general case of random noise with arbitrary correlation time, yielding a fully consistent new theory for non-Markovian systems. We also address the question of computability of the joint response-excitation probability density function as a solution to a boundary value problem involving only one differential constraint. By means of a simple analytical example, it is shown that, in general, such a problem is undetermined, in the sense that it admits an infinite number of solutions. This issue can be overcome by completing the system with additional relations yielding a closure problem, which is similar to the one arising in the standard response theory. Numerical verification of the equations for the joint response-excitation density is obtained for a tumour cell growth model under immune response.
Dual origins of social parasitism in North American Dialictus (Hymenoptera: Halictidae) confirmed using a phylogenetic approach
Authors: Gibbs Jason , Albert Jennifer , Packer Laurence 
Published: November 2011

AbstractThe bee subgenus Dialictus (Halictidae: Lasioglossum) displays a large array of behaviours including solitary behaviour, eusociality, and social parasitism. Socially parasitic Dialictus share a suite of morphological traits; these could result from shared ancestry, but given their functional significance, could also have resulted from adaptive convergence. A combined morphological and molecular phylogenetic approach was used to test for monophyly of North American socially parasitic Dialictus. Two data sets were used in the phylogenetic analyses. First, short mitochondrial DNA sequences from previous taxonomic studies of North American Dialictus, including six social parasites, were used because of the broad taxon sampling they provide. These data were analysed in combination with a set of 40 morphological characters, including a large proportion of characters associated with social parasitism. Phylogenetic analysis of the combined DNA barcode and morphology data set resolves two distinct lineages of social parasite. The second data set was based on three genes (cytochrome c oxidase subunit 1, elongation factor 1α, and long‐wavelength rhodopsin), but with sparser taxon sampling, including one representative from each putative social parasite‐lineage. This also supported dual origins of social parasitism among North American Dialictus. The evolution of social parasitism is discussed.© The Willi Hennig Society 2011.
Complete deficiency of the sixth complement component (C6Q0), susceptibility to Neisseria meningitidis infections and analysis of the frequencies of C6Q0 gene defects in South Africans
Authors: Orren A , Owen E P , Henderson H E , van der Merwe L , Leisegang F , Stassen C , Potter P C 
Published: November 2011

Summary
Complete complement component 6 deficiency (C6Q0) is a co-dominant genetic disease presenting as increased susceptibility to invasive Neisseria meningitidis infections. Affected individuals have two affected alleles which can be homozygous or compound heterozygous for the particular gene defects they carry. This disorder has been diagnosed relatively frequently in Western Cape South Africans. Affected patients are prescribed penicillin prophylaxis. In 2004 we commenced a clinical follow-up study of 46 patients. Of these, 43 had family age-matched C6 sufficient controls. Participants were classified as either (i) well, or (ii) having a serious illness (SI) or died (D). An SI was a long-term illness that did not allow the performance of normal daily activities. Among 43 patients, 21 were well and 22 were SI/D, while among 43 matched controls, 35 were well and eight were SI/D. This difference is highly significant. Among all 46 C6Q0 patients, those who had had recurrent infection had significantly more SI/D than those who had suffered none or one infection. Thus, this work demonstrates the long-term serious outcome of repeated meningococcal disease (MD) episodes. We investigated the frequencies of four C6Q0 pathogenic mutations known to affect Cape patients (828delG, 1138delC, 821delA and 1879delG) in 2250 newborns. A total of 103 defective alleles (2·28%) and three affected C6Q0 individuals were detected. For all defects combined, 5·24 affected subjects (C6Q0) are expected among 10 000 individuals. What is still unknown is the number of C6Q0 individuals who suffer MD or other infectious diseases.
Inorganic phosphate and FGF‐23 predict outcome in stable systolic heart failure
Authors: Plischke Max , Neuhold Stephanie , Adlbrecht Christopher , Bielesz Bernhard , Shayganfar Sascha , Bieglmayer Christian , Szekeres Thomas , Hörl Walter H. , Strunk Guido , Vavken Patrick , Pacher Richard , Hülsmann Martin 
Published: November 2011

Eur J Clin Invest 2012; 42 (6): 649–656AbstractBackground  Recent studies show associations between inorganic phosphate and risk of heart failure in the general population as well as between fibroblast growth factor 23 (FGF‐23) and outcome in coronary heart disease. This study was carried out to assess whether circulating levels of inorganic phosphate and FGF‐23, a new central hormone in mineral bone metabolism, predict outcome in systolic heart failure.Materials and methods  Ninety‐nine consecutive outpatients with systolic heart failure were enrolled. Mean (SD) age was 61 years (11), mean left ventricular ejection fraction (LVEF) was 33% (10), 82 patients were men, median estimated creatinine clearance was 83 mL/min (Q1–Q3 58–106), median NTproBNP level was 803 pg/mL (Q1–Q3 404–2757), median inorganic phosphate was 1·12 mM (Q1–Q3 1·02–1·22), median FGF‐23 was 39·02 pg/mL (Q1–Q3 32·45–55·86) and median follow‐up was 35 months. Associations between inorganic phosphate, FGF‐23 and endpoints were assessed using Cox regression analyses.Results  Inorganic phosphate and FGF‐23 levels were significantly higher (P < 0·001 and P = 0·009) in patients reaching the combined endpoint of cardiac hospitalization or death. FGF‐23 (ln) predicted all‐cause mortality (hazard ratio (HR) 5·042, P = 0·032) in a model adjusted for age, gender, estimated creatinine clearance, LVEF, New York Heart Association (NYHA) stage and NTproBNP level. Inorganic phosphate predicted heart failure hospitalization (HR 26·944, P = 0·021), cardiac hospitalization (HR 16·016, P = 0·017) and the combined endpoint (HR 13·294, P = 0·015) in models adjusted for the same co‐variables.Conclusion  The results of this study demonstrate the independent prognostic value of inorganic phosphate and FGF‐23 in heart failure even in the context of established risk markers.
Review of theoretical developments in stream ecology and their influence on stream classification and conservation planning
Authors: MELLES S. J. , JONES N. E. , SCHMIDT B. 
Published: November 2011

Summary1. We review some of the classic literature on geomorphology and ecology of streams in an effort to examine how theoretical developments in these aquatic sciences have influenced the way fresh flowing waters are classified. Our aim was to provide a historical examination of conceptual developments related to fluvial classification, and to discuss implications for conservation planning and resource management.2. Periods of conceptual influences can be separated into three overlapping phases each distinguished by theoretical, analytical or technological advances: (i) early Darwinian perspectives; (ii) the quantitative revolution; and, (iii) age of the computer, hierarchy and scale.3. During the first phase, stream geomorphologists were largely influenced by Darwinian metaphors. The study of stream origin and change through time became more important than the study of stream systems themselves. The idea that streams progress deterministically through successive stages of development seemed to create a veil, most prevalently in North America, that barred analysis of the full scope of variability in these systems for over 50 years.4. The quantitative revolution brought about many new ideas and developments, including the laws of stream numbers. This period focused on predictive and mechanistic explanations of stream processes, setting the stage for physically based stream classifications that assume that streams can be restored by engineering their physical characteristics.5. In the most recent ‘age of the computer’, concepts from the fields of geographic information science and landscape ecology have been incorporated into stream ecology and aquatic classification. This has led to investigations in stream and aquatic ecosystems at hierarchical spatial scales and along different dimensions (upstream/downstream, riparian/floodplain, channel/ground water and through time). Yet, in contrast to terrestrial landscapes, flowing waters are not as easily classified into spatially nested hierarchical regions wherein upper levels can be subdivided into smaller and smaller regions at finer spatial scales. Riverscapes are perhaps best described as directionally nested hierarchies: aquatic elements further downstream cannot be rendered equivalently to elements upstream. Moreover, fully integrated aquatic ecosystem classifications that incorporate lake and river networks, wetlands, groundwater reservoirs and upland areas are exceedingly rare.6. We reason that the way forward for classification of flowing waters is to account for the directionally nested nature of these networks and to encode flexibility into modern digital freshwater inventories and fluvial classification models.
Economic modelling of an integrated grazed and conserved perennial ryegrass forage production system
Authors: Finneran E. , Crosson P. , O’Kiely P. , Shalloo L. , Forristal P. D. , Wallace M. 
Published: November 2011

AbstractThe Grange Feed Costing Model was modified to simulate the economic implications of grassland management strategies for a grass‐based suckler beef calf‐to‐weanling system at the whole‐farm level. The modified model enabled costing of annual grass consumed as grazed grass and silage when the farm grazing and conservation areas are integrated. Grass growth data from sites in the south, east and north of Ireland were used. Sixty‐three scenarios were simulated, enabling analysis of site, stocking rate and silage strategy effects on total annual feed cost for the grass forage production system. Total annual feed cost (of grazed grass and grass silage) ranged from €96 to €111 per 1000 UFL (Unité Fourragère Lait) and €411 to €456 per beef cow unit (CU). The silage strategy with respect to the number of harvests and whether the silage area was grazed in the spring had negligible impact on annual total feed cost per CU. However, a tendency towards reduced annual feed cost under a two harvest, relative to a one harvest, silage strategy was observed. The lowest cost stocking rate was 2 CU ha−1. Site‐specific differences such as seasonal growth distribution and nitrogen fertilizer response rate had the greatest influence on the annual cost of the grass‐based feeding system.
Expression of calretinin by breast carcinoma and the potential for misdiagnosis of mesothelioma
Authors: Powell George , Roche Heather , Roche William R 
Published: November 2011

Powell G, Roche H & Roche W R  (2011) Histopathology59, 950–956Expression of calretinin by breast carcinoma and the potential for misdiagnosis of mesotheliomaAims:  Calretinin and cytokeratin (CK)5/6 are frequently used to differentiate between metastatic breast cancer and primary malignant mesothelioma in pleural biopsies, but both tumours may express these markers. This study was aimed at evaluating the frequency of calretinin expression in primary breast carcinomas, and assessing the characteristics of the calretinin‐positive tumours.Methods and results:  Fifty‐three primary breast adenocarcinomas were analysed for immunohistochemical expression of calretinin. CK5/6 and epidermal growth factor receptor (EGFR) immunostaining were performed on the calretinin‐positive subset. Tumours were classified as basal‐like if they met standard morphological and immunohistochemical criteria. Fifteen per cent (8/53) of the breast tumours were positive for calretinin. Eighty‐eight per cent (7/8) of the calretinin‐positive tumours were grade 3, as compared with 20% (9/45) of the calretinin‐negative tumours (P < 0.001). Only 13% (1/8) of the calretinin‐positive tumours were also oestrogen receptor (ER)‐positive, as compared with 87% (39/45) of the calretinin‐negative tumours (P < 0.001). Eleven per cent (6/53) of the tumours were classified as basal‐like. Of these, four were positive for calretinin and two were negative (P = 0.003).Conclusions:  Fifteen per cent of breast carcinomas stain with calretinin. These tumours are more likely to be high‐grade, ER‐negative, and display a basal‐like phenotype. These tumours may be misdiagnosed as malignant mesothelioma when they metastasize to the pleura.
Factors influencing the agreement on histopathological assessments of breast biopsies among pathologists
Authors: Stang Andreas , Trocchi Pietro , Ruschke Kathrin , Schmidt‐Pokrzywniak Andrea , Holzhausen Hans‐Jürgen , Löning Thomas , Buchmann Jörg , Thomssen Christoph , Lantzsch Tillmann , Hauptmann Steffen , Böcker Werner , Kluttig Alexander 
Published: November 2011

Stang A, Trocchi P, Ruschke K, Schmidt‐Pokrzywniak A, Holzhausen H‐J, Löning T, Buchmann J, Thomssen C, Lantzsch T, Hauptmann S, Böcker W & Kluttig A  (2011) Histopathology 59, 939–949  Factors influencing the agreement on histopathological assessments of breast biopsies among pathologistsAims:  It has been recommended that the histopathology results of core biopsies of the breast are categorized according to the B‐categorization scheme. We measured the interobserver variability of the B‐categorization of core biopsies of the breast.Methods and results:  Core biopsies were taken among 765 women at the University of Halle between 2006 and 2008. All histological slides were reviewed in a blinded fashion by two experienced breast pathologists. We calculated observed and chance‐corrected agreements (kappa) and 95% confidence intervals (CI). The prevalence of B3–B5 biopsies was 41.6%. The observed and weighted kappa agreement of the five‐level B‐categorization scheme was 0.87 (95% CI: 0.84 −0.89) and 0.89 (95% CI: 0.89–0.91), respectively. The most frequent disagreement was between B2 and B3 (47 of 103 disagreements, 45.6%). Overall, 49.5% of all disagreements were clinically relevant disagreements that would imply different therapeutic strategies. Agreement was modified by referral group, Breast Imaging Reporting and Data System (BIRADS) level, radiological breast density, imaging guidance and application of immunohistological staining.Conclusions:  Interobserver agreement of the B‐categorization scheme was high and was modified by referral status, level of radiological suspicion of breast cancer, breast density, imaging guidance of core biopsies and requirement of additional immunohistological staining.
Mesothelial markers in high‐grade breast carcinoma
Authors: Duhig Edwina E , Kalpakos Lydia , Yang Ian A , Clarke Belinda E 
Published: November 2011

Duhig E E, Kalpakos L, Yang I A & Clarke B E  (2011) Histopathology59, 957–964Mesothelial markers in high‐grade breast carcinomaAims:  Advances in molecular profiling have subdivided breast carcinomas into distinct subtypes. Basal carcinomas are generally oestrogen receptor (ER)−progesterone receptor (PR)−/human epidermal growth factor receptor 2 (HER2)−, and cytokeratin (CK)5/6+. This profile overlaps with that of mesothelial cells. This study of high‐grade breast carcinomas was undertaken to determine the expression of mesothelial markers.Methods and results:  Immunohistochemistry was performed on 23 basal‐like breast carcinomas and 30 high‐grade breast carcinomas with variable ER, PR and HER2 expression. The incidence of staining of CK5/6, CK14, calretinin, Wilms’ tumour 1 (WT1), thrombomodulin and epithelial membrane antigen was assessed statistically. CK14 staining was more specifically associated with triple‐negative tumours than CK5/6. Calretinin positivity was statistically associated with basal‐like carcinomas. WT1 and thrombomodulin expression was infrequent and limited to a small number of non‐basal carcinomas.Conclusions:  There is an overlap between the immunophenotype of mesothelial cells and that of basal‐like carcinomas of breast. Positive calretinin and CK5/6 are not specific, and may be seen in both mesothelial cells and basal‐like breast carcinomas. Negative ER and PR of basal carcinomas may also bias the observer against a breast origin. However, other negative mesothelial markers, such as WT1 and thrombomodulin, may help point to the correct diagnosis.
In breast cancer, a high ratio of tumour‐infiltrating intraepithelial CD8+ to FoxP3+ cells is characteristic for the medullary subtype
Authors: Anz David , Eiber Stephan , Scholz Christoph , Endres Stefan , Kirchner Thomas , Bourquin Carole , Mayr Doris 
Published: November 2011

Anz D, Eiber S, Scholz C, Endres S, Kirchner T, Bourquin C & Mayr D  (2011) Histopathology59, 965–974In breast cancer, a high ratio of tumour‐infiltrating intraepithelial CD8+ to FoxP3+ cells is characteristic for the medullary subtypeAims:  Medullary breast cancer (MBC) is a biologically distinct subtype of breast cancer characterized by prominent lymphocytic infiltrates and a favourable clinical outcome. Tumour‐infiltrating CD8+ effector T cells may contribute to the good prognosis of this type of cancer; however, certain subtypes of lymphocyte, such as FoxP3+ regulatory T cells (Tregs), can also suppress antitumour immunity.Methods and results:  We determined tumour infiltration by FoxP3+, CCL22+ and CD8+ cells in paraffin‐embedded sections of MBC, and, as a reference, in samples of grade 3 ductal, lobular and mucinous breast cancer. All analysed MBCs were strongly infiltrated by FoxP3+ cells, whereas only weak infiltrates were detected in ductal or lobular breast cancer. This finding was unexpected, given the good prognosis of MBC. Strikingly, the number of CD8+ T cells exceeded the number of FoxP3+ cells in MBC (ratio of CD8+ to FoxP3+ cells of 2.6), whereas equal amounts of both cell types were found in ductal breast cancer (ratio of CD8+ to FoxP3+ cells of 1.1). In both types of breast cancer, we also detected cells expressing the Treg‐attracting chemokine CCL22.Conclusions:  In breast cancer, a predominance of tumour‐infiltrating CD8+ over FoxP3+ cells was observed in MBC. Thus, the ratio of CD8+ to FoxP3+ cells rather than the absolute number of intratumoral FoxP3+ cells may be predictive for the clinical outcome of cancer.