bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice
Authors: Zou Cheng , Lehti-Shiu Melissa D. , Thibaud-Nissen Françoise , Prakash Tanmay , Buell C. Robin , Shiu Shin-Han 
Published: July 2009

Abstract
Pseudogenes (Ψ) are nonfunctional genomic sequences resembling functional genes. Knowledge of Ψs can improve genome annotation and our understanding of genome evolution. However, there has been relatively little systemic study of Ψs in plants. In this study, we characterized the evolution and expression patterns of Ψs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). In contrast to animal Ψs, many plant Ψs experienced much stronger purifying selection. In addition, plant Ψs experiencing stronger selective constraints tend to be derived from relatively ancient duplicates, suggesting that they were functional for a relatively long time but became Ψs recently. Interestingly, the regions 5′ to the first stops in the Ψs have experienced stronger selective constraints compared with 3′ regions, suggesting that the 5′ regions were functional for a longer period of time after the premature stops appeared. We found that few Ψs have expression evidence, and their expression levels tend to be lower compared with annotated genes. Furthermore, Ψs with expressed sequence tags tend to be derived from relatively recent duplication events, indicating that Ψ expression may be due to insufficient time for complete degeneration of regulatory signals. Finally, larger protein domain families have significantly more Ψs in general. However, while families involved in environmental stress responses have a significant excess of Ψs, transcription factors and receptor-like kinases have lower than expected numbers of Ψs, consistent with their elevated retention rate in plant genomes. Our findings illustrate peculiar properties of plant Ψs, providing additional insight into the evolution of duplicate genes and benefiting future genome annotation.
Are South Africa's cities changing? Indications from the mid‐1990s
Authors: Seekings Jeremy 
Published: July 2009

Books reviewed in this article:Scott A. Bollens, Urban peace‐building in divided societies: Belfast and JohannesburgAlan Morris, Bleakness and light: inner‐city transition in Hillbrow, JohannesburgRobert Cameron, Democratisation of South African local government: a tale of three citiesSusan Parnell, Edgar Pieterse, Mark Swilling and Dominique Wooldridge (eds.), Democratising local government: the South African experimentGrant R. Saff, Changing Cape Town: urban dynamics, policy and planning during the political transition in South Africa
Epidermolysis bullosa nevus arising in a patient with Dowling–Meara type epidermolysis bullosa simplex with a novel K5 mutation
Authors: SUGIYAMA‐FUKAMATSU Hiroko , SUZUKI Norihiro , NAKANISHI Gen , IWATSUKI Keiji 
Published: July 2009

AbstractWe report herein a 4‐year‐old girl with Dowling–Meara type epidermolysis bullosa (EB) who presented with peculiar pigmented nevi. Blister formation had repeatedly occurred on the erythematous plaques in a circinate fashion since birth, and marked hyperkeratosis was observed on the palms and soles associated with nail deformity. Her mother and maternal grandmother also had similar symptoms. In addition to the blistering lesions, the patient had three large, asymmetrical, pigmented plaques with color variegation. Light and electron microscopic findings of the blistering lesions showed a subepidermal blister with intracytoplasmic granules in keratinocytes as well as degeneration of basal cells and aggregation of tonofilaments. The pigmented lesions revealed histopathological features of compound nevus without malignant changes. Gene analysis revealed an E478K (Glu to Lys) mutation in exon 5 of the keratin 5 (K5) gene. These findings, together with clinical features, were consistent with those of Dowling–Meara type EB associated with so‐called EB nevus.
Case of follicular mucinosis: Nestin‐expression in mucin‐producing cells
Authors: SAKUMA Hiroyuki , AMOH Yasuyuki , NIIYAMA Shiro , KANOH Maho , KATSUOKA Kensei 
Published: July 2009

AbstractA 29‐year‐old Japanese man had an asymptomatic, solitary, indurated, erythematous plaque measuring 30 mm × 30 mm on his jaw that had been present for a month. The skin lesion had follicular hyperkeratosis, and lacked hair. A skin biopsy specimen showed a dense perifollicular infiltration composed of lymphocytes, with an admixture of eosinophils in the full thickness of the dermis. The hair follicles and sebaceous glands had reticular epithelial degeneration by mucoid material of the outer root sheath and sebaceous epithelium. The mucoid material stained with Alcian blue at pH 2.5. The clinical and histological features were consistent with the diagnosis of follicular mucinosis. On immunohistochemistry, the outer root sheath cells with reticular epithelial degeneration were nestin‐positive and keratin 15‐negative. These results suggest that the outer root sheath cells with reticular epithelial degeneration come from the nestin‐positive, multipotent, hair follicle stem cells.
Human papillomavirus 16-specific T cell responses in classic HPV-related vulvar intra-epithelial neoplasia. Determination of strongly immunogenic regions from E6 and E7 proteins
Authors: Bourgault Villada I , Moyal Barracco M , Berville S , Bafounta M L , Longvert C , Prémel V , Villefroy P , Jullian E , Clerici T , Paniel B , Maillère B , Choppin J , Guillet J G 
Published: July 2009

SummaryCell-mediated immunity directed against human papillomavirus 16 (HPV-16) antigens was studied in 16 patients affected with classic vulvar intra-epithelial neoplasia (VIN), also known as bowenoid papulosis (BP). Ten patients had blood lymphocyte proliferative T cell responses directed against E6/2 (14–34) and/or E6/4 (45–68) peptides, which were identified in the present study as immunodominant among HPV-16 E6 and E7 large peptides. Ex vivo enzyme-linked immunospot–interferon (IFN)-γ assay was positive in three patients who had proliferative responses. Twelve months later, proliferative T cell responses remained detectable in only six women and the immunodominant antigens remained the E6/2 (14–34) and E6/4 (45–68) peptides. The latter large fragments of peptides contained many epitopes able to bind to at least seven human leucocyte antigen (HLA) class I molecules and were strong binders to seven HLA-DR class II molecules. In order to build a therapeutic anti-HPV-16 vaccine, E6/2 (14–34) and E6/4 (45–68) fragments thus appear to be good candidates to increase HPV-specific effector T lymphocyte responses and clear classic VIN (BP) disease lesions.
Determinants of biodiversity in subtropical shallow lakes (Atlantic coast, Uruguay)
Authors: KRUK CARLA , RODRÍGUEZ‐GALLEGO LORENA , MEERHOFF MARIANA , QUINTANS FEDERICO , LACEROT GISSELL , MAZZEO NÉSTOR , SCASSO FLAVIO , PAGGI JUAN C. , PEETERS EDWIN T. H. M. , MARTEN SCHEFFER 
Published: July 2009

Summary1. Shallow lakes and ponds contribute disproportionally to species richness relative to other aquatic ecosystems. In‐lake conditions (e.g. presence of submerged plants) seem to play a key role in determining diversity, as has been demonstrated for temperate lakes. When water quality deteriorates and turbidity increases, conditions in such lakes are affected drastically resulting in a loss of diversity. However, it is not clear whether subtropical lakes show the same pattern and whether the richness of all groups reacts similarly to environmental changes.2. Our aim was to analyse the main factors explaining patterns of species richness in plankton, fish and submerged macrophyte assemblages in both turbid and clear subtropical shallow lakes. We analysed abiotic and biotic features of 18 subtropical, small‐ to medium‐sized, shallow lakes along the Uruguayan coast. We compared both turbid and clear ecosystem states and evaluated the relative variance explained by the factors measured.3. Variables describing lake and catchment morphology, as well as the percentage of the water column occupied by submerged macrophytes (%PVI) and water turbidity, had strong effects on taxon richness. Interestingly, individual biotic groups had dissimilar richness patterns. Macrophyte %PVI decreased with increasing lake area, while fish species richness showed the opposite pattern. Phytoplankton species richness increased with macrophyte %PVI, while the zooplankton richness pattern varied depending on the taxonomic group considered.4. Overall, our results indicate that, as found for temperate lakes, a greater submerged plant cover promotes higher species richness in several groups, and that this may overwhelm the otherwise expected positive effect of lake size on species richness. On the other hand, small‐bodied zooplankton predominated in lakes with high plant abundance. Our findings concur with recent studies, indicating that refuge capacity of aquatic plants might be weaker in (sub)tropical than in temperate shallow lakes.5. The extremely high plant cover, frequently observed in warm lakes, could potentially lead to different richness patterns in some groups. This conclusion has important consequences for local managers and conservationists.
Chromosomal abnormalities determined by comparative genomic hybridization are helpful in the diagnosis of atypical hepatocellular neoplasms
Authors: Kakar Sanjay , Chen Xin , Ho Coral , Burgart Lawrence J , Adeyi Oyedele , Jain Dhanpat , Sahai Viabhav , Ferrell Linda D 
Published: July 2009

Aims:  To explore the utility of cytogenetic abnormalities in the distinction of hepatic adenoma (HA) and well‐differentiated hepatocellular carcinoma (HCC).Methods and results:  Array‐based comparative genomic hybridization (CGH) was used to determine chromosomal abnormalities in 39 hepatocellular neoplasms: 12 HA, 15 atypical hepatocellular neoplasms (AHN) and 12 well‐differentiated HCC. The designation of AHN was used in two situations: (i) adenoma‐like neoplasms (n = 8) in male patients (any age) and women >50 years and <15 years old; (ii) adenoma‐like neoplasms with focal atypical features (n = 7). CGH abnormalities were seen in none of the HAs (0/12), eight (53%) AHNs and 11 (92%) HCCs. The number and nature of abnormalities in AHN was similar to HCC with gains in 1q, 8q and 7q being the most common. Although follow‐up information was limited, recurrence and/or metastasis were observed in three AHNs (two with abnormal, one with normal CGH).Conclusions:  Adenoma‐like neoplasms with focal atypical morphological features or unusual clinical settings such as male gender or women outside the 15–50 year age group can show chromosomal abnormalities similar to well‐differentiated HCC. Even though these tumours morphologically mimic adenoma, they can recur and metastasize. Determination of chromosomal abnormalities can be useful in the diagnosis of AHN.
Guanylyl cyclase C is a specific marker for differentiating primary and metastatic ovarian mucinous neoplasms
Authors: Ciocca Vincenzo , Bombonati Alessandro , Palazzo Juan P , Schulz Stephanie , Waldman Scott A 
Published: July 2009

Aims: The aim was to assess the value of GCC in distinguishing primary ovarian mucinous neoplasms from metastatic mucinous adenocarcinomas with ovarian involvement. Guanylyl cyclase C (GCC) is a brush border membrane receptor for the endogenous peptides guanylin and uroguanylin, and the homologous diarrhoeagenic bacterial heat‐stable enterotoxins that is selectively expressed by epithelial cells from the duodenum to the rectum, but not by normal epithelia of the stomach or oesophagus, or normal extramucosal cells in humans.Methods and results: Fifty ovarian tumours: 27 primary ovarian mucinous neoplasms (seven cystadenomas, 10 borderline tumours and 10 cystadenocarcinomas) and 23 metastatic mucinous adenocarcinomas with ovarian involvement [13 colorectal adenocarcinomas, four gastric adenocarcinomas, six appendiceal mucinous tumours (four adenocarcinomas, one with neuroendocrine features, and two appendiceal mucinous cystadenomas)] were studied. For primary ovarian mucinous neoplasms, 25 of 27 were negative for GCC. Twelve of 13 cases of colorectal adenocarcinoma (except for one neuroendocrine adenocarcinoma) were positive for GCC. Three of four appendiceal mucinous adenocarcinomas were positive for GCC in both the primary and metastatic tumours (except for one neuroendocrine adenocarcinoma). Two of two appendiceal mucinous cystadenomas were positive for GCC. Of four cases of gastric adenocarcinoma with ovarian involvement, only one (primary tumour) exhibited focal GCC staining.Conclusions: GCC is a useful marker for differentiating between primary and secondary ovarian mucinous neoplasms.
Neutrophil/eosinophil‐rich type of primary cutaneous anaplastic large cell lymphoma: a clinicopathological, immunophenotypic and molecular study of nine cases
Authors: Kong Yun‐Yi , Dai Bo , Kong Jin‐Cheng , Lu Hong‐Fen , Shi Da‐Ren 
Published: July 2009

Aims:  To elucidate the clinicopathological, immunophenotypic and molecular features of neutrophil/eosinophil‐rich primary cutaneous anaplastic large cell lymphoma (CALCL), and to emphasize the cutaneous manifestations, differential diagnosis and prognosis of this peculiar entity.Methods and results:  We described the clinical presentations, histopathology, immunophenotype, molecular features and follow‐up courses of nine neutrophil/eosinophil‐rich CALCL cases. Various clinical lesions including multiple nodules, plaques and solitary exophytic masses with or without ulceration or crusting were noted in nine patients. Two patients died of disease progression, with one developing multiple lymph node involvement. Histologically, cohesive sheets or small clusters of neoplastic cells were admixed with large numbers of neutrophils and/or eosinophils, representing 10–40% of cells per high‐power field. All nine cases showed T‐cell phenotypes. The frequency of rearranged TCRB, TCRG and TCRD genes in six cases with available paraffin‐embedded tissue was 100%, 83% and 33%, respectively.Conclusions:  Neutrophil/eosinophil‐rich CALCL should be differentiated from various infectious and non‐infectious diseases, especially from non‐neoplastic cutaneous CD30+ infiltrates rich in neutrophils and eosinophils. Precise correlation of clinical presentation, morphological features, phenotypic and molecular analysis can help to establish the correct diagnosis. Whether this rare variant has a significantly different prognosis from classical CALCL needs further investigation.
The pathology of depopulated bovine ureter xenografts utilized for vascular access in haemodialysis patients
Authors: Kingston Gearoid T , Darby Christopher R , Roberts Ian S D 
Published: July 2009

Aims:  Vascular access for long‐term haemodialysis is obtained through the surgical fashioning of arteriovenous fistulae, utilizing the patients’ native blood vessels, or by insertion of synthetic grafts or non‐synthetic gluteraldehyde cross‐linked biological xenografts. These non‐native grafts have high complication rates and a depopulated bovine ureter xenograft has recently been developed as an alternative. The aim was to undertake the first systematic review of the histopathology of bovine ureter xenografts (n = 25) utilized for haemodialysis vascular access in humans.Methods and results:  Pre‐insertion specimens (n = 7) showed preservation of some cellular architecture and histological antigenicity. Uncomplicated segments of post‐insertion specimens (n = 18) showed myofibroblastic in‐growth but no luminal endothelialization and no vascularization of the wall, other than at sites of needle puncture. Post‐insertion, 50% showed a severe adventitial host inflammatory response with a dominant granulomatous and eosinophil‐rich infiltrate. Inflammation was present in grafts with various complications (stenosis, thrombosis, aneurysm), but there was no clear pathogenic link.Conclusions:  We conclude that repopulation of bovine ureter xenografts by host cells is limited and that, in specimens removed for complications, an inflammatory reaction to the xenograft is common. This could reflect retention of some antigenicity following pre‐insertion ‘depopulation’ of the grafts.
Urothelial carcinoma following augmentation cystoplasty: an aggressive variant with distinct clinicopathological characteristics and molecular genetic alterations
Authors: Sung Ming‐Tse , Zhang Shaobo , Lopez‐Beltran Antonio , Montironi Rodolfo , Wang Mingsheng , Davidson Darrell D , Koch Michael O , Cain Mark P , Rink Richard C , Cheng Liang 
Published: July 2009

Aims:  Patients who have undergone intestinal augmentation cystoplasty are at risk for developing latent vesicle malignancy. The aim was to evaluate the histological and immunohistochemical characteristics and molecular genetic alterations in these neoplasms.Methods and results:  Four patients developing urothelial neoplasms after augmentation cystoplasty were included in the current study. The mean age of the patients, including two men and two women, was 37 years. The latency from bladder augmentation to developing malignancy ranged from 17 to 21 years (mean 19 years). All patients died of cancer shortly after diagnosis (mean 5 months). In the morphological evaluation, all tumours were high‐grade (grade 3) invasive urothelial carcinoma comprising various architectural patterns with brisk mitoses and tumour necrosis. Three harboured glandular differentiation and the remaining one showed squamous differentiation. All cases revealed abnormal decreasing β‐catenin expression. Two tumours showed nuclear expression of CDX2. On UroVysion fluorescence in situ hybridization (FISH) analysis, all tumours displayed characteristic chromosomal abnormalities. Point mutations of both FGFR3 and p53 genes were identified in one case.Conclusions:  Urothelial carcinomas developed after augmentation cystoplasty are extremely aggressive and exhibit distinct morphological, immunohistochemical and genetic characteristics. UroVysion FISH analysis may offer a surveillance strategy in patients who undergo augmentation cystoplasty.
New opportunities for an old method: using fluorescent colours to measure seed dispersal
Authors: Lemke Andreas , Von Der Lippe Moritz , Kowarik Ingo 
Published: July 2009

Summary 1. Seed dispersal is of high applied relevance as it governs colonization processes in rare species and during plant invasions. Seed tracking is a powerful approach to analysing dispersal processes and usually requires seed tagging. Marking diaspores with fluorescent colours is a promising tagging method, but comes with several technical limitations. 2. We analysed the durability of different colours, associated changes in weight gain and lift‐off velocity, visibility under ultraviolet (UV) light and recapture rates for different diaspore types (samaras, plumed diaspores and small, round diaspores). 3. Weight gain ranged from 20% to 61% and loss of colour after 1 month of outdoor exposure ranged from 1% to 31%, with airbrush technique offering the best retention of colour, followed by pigment colour application and common aerosol spray treatment. Seed tagging with aerosol spray paint or by airbrush technique increased the lift‐off velocity of samaras by 6–7%. 4. Good results for recapture experiments with fluorescently marked diaspores can be achieved using UV torches: large diaspores are visible at distances of up to 8 m in open habitats, and small diaspores up to 3·5 m. Recapture rates on asphalt and grass lawn were close to 100% for large diaspores, and ranged from 85% to 90% for other diaspores. An area of c. 0·1 ha could by thoroughly searched within 1 h. 5. Pigment colour application is suitable for large diaspores (>3 cm in length). Aerosol spray application is easy but induces a high weight gain and is practicable only for use over short sampling periods. Airbrush application requires special equipment but combines the advantages of low weight gain and high durability and is even appropriate for plumed diaspores. 6. Synthesis and applications. Our study revealed strengths and weaknesses of different methods of tagging diaspores with fluorescent colours. Quantifying the changes that colouring has on seed traits helps to reduce data bias, especially in modelling. The choice of the appropriate tagging method combined with the use of modern UV torches provides considerable methodological advance in studying seed dispersal over long distances and could improve studies on colonization processes of endangered species and on plant invasions.
Phyloecology of urban alien floras
Authors: Ricotta Carlo , La Sorte Frank A. , Pyšek Petr , Rapson G.L. , Celesti‐Grapow Laura , Thompson Ken 
Published: July 2009

Summary 1.  Understanding the mechanisms that affect invasion success of alien species is a major issue in current ecological research. Although many studies have searched for either functional or habitat attributes that drive invasion mechanisms, few researchers have addressed the role of phylogenetic diversity of alien species. 2.  Here, using data from 21 urban floras located in Europe and eight in the USA, we show that the phylogenetic diversity of alien species is significantly lower than that of native species, both at the continental scale and at the scale of single cities. 3.  Second, we show that if archaeophytes and neophytes (non‐native species introduced into Europe before and after AD 1500, respectively) are analysed separately, archaeophytes show lower phylogenetic diversity than neophytes, while the phylogenetic structure of neophytes is indistinguishable from a random sample of species from the entire species pool. 4.  Our results suggest that urban aliens are subject to environmental filters that constrain their phylogenetic diversity, although these filters act more strongly upon archaeophytes than neophytes. 5.
Synthesis. Despite the huge taxonomic diversity of plants imported into European and American cities, the strong environmental filters imposed by cities constrain the functional diversity of urban floras, which is reflected in their generally low phylogenetic diversity. Urban alien floras are mainly composed of phylogenetically related species that are well adapted to anthropogenic habitats, although these filters are stronger for species groups with longer residence times.
Development of thyroid diseases in the treatment of chronic hepatitis C with α‐interferon may be a good prognosticator in achieving a sustained virological response: A meta‐analysis
Authors: Tran Huy Anh , Malcolm Reeves Glenn Edward , Gibson Robert , Attia John Richard 
Published: July 2009

AbstractBackground and Aim:  Thyroid dysfunction is the most common endocrinopathy associated with hepatitis C and its interferon‐based treatment. When undergoing treatment, interferon and ribavirin synergize to potently stimulate the immune system in order to eradicate the virus. One of the innocent bystanders in this accentuated response is the thyroid. The present study investigated whether thyroid dysfunction while undergoing combination treatment for hepatitis C is a favorable prognostic maker for a sustained virological response.Methods:  We carried out a prospective clinical audit in 201 patients treated with combination ribavirin and α‐interferon and determined the prevalence of sustained virological response in patients in association with thyroid disease. A meta‐analysis was also carried out pooling 741 patients from four previous studies on this topic.Results:  There was positive and significant association between thyroid disease and viral clearance. This was not supported by the meta‐analysis, however, and some plausible explanations are proffered for this inconsistency.Conclusion:  Despite lacking supportive evidence from the meta‐analysis, it is important that this information is confirmed (or refuted) in future studies.