bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical similarities and differences of patients with X-linked lymphoproliferative syndrome type 1 (XLP-1/SAP deficiency) versus type 2 (XLP-2/XIAP deficiency)
Authors: Schmid Jana Pachlopnik , Canioni Danielle , Moshous Despina , Touzot Fabien , Mahlaoui Nizar , Hauck Fabian , Kanegane Hirokazu , Lopez-Granados Eduardo , Mejstrikova Ester , Pellier Isabelle , Galicier Lionel , Galambrun Claire , Barlogis Vincent , Bordigoni Pierre , Fourmaintraux Alain , Hamidou Mohamed , Dabadie Alain , Le Deist Françoise , Haerynck Filomeen , Ouachée-Chardin Marie , Rohrlich Pierre , Stephan Jean-Louis , Lenoir Christelle , Rigaud Stéphanie , Lambert Nathalie , Milili Michèle , Schiff Claudin , Chapel Helen , Picard Capucine , de Saint Basile Geneviève , Blanche Stéphane , Fischer Alain , Latour Sylvain 
Published: November 2010

Abstract
X-linked lymphoproliferative syndromes (XLP) are primary immunodeficiencies characterized by a particular vulnerability toward Epstein-Barr virus infection, frequently resulting in hemophagocytic lymphohistiocytosis (HLH). XLP type 1 (XLP-1) is caused by mutations in the gene SH2D1A (also named SAP), whereas mutations in the gene XIAP underlie XLP type 2 (XLP-2). Here, a comparison of the clinical phenotypes associated with XLP-1 and XLP-2 was performed in cohorts of 33 and 30 patients, respectively. HLH (XLP-1, 55%; XLP-2, 76%) and hypogammaglobulinemia (XLP-1, 67%; XLP-2, 33%) occurred in both groups. Epstein-Barr virus infection in XLP-1 and XLP-2 was the common trigger of HLH (XLP-1, 92%; XLP-2, 83%). Survival rates and mean ages at the first HLH episode did not differ for both groups, but HLH was more severe with lethal outcome in XLP-1 (XLP-1, 61%; XLP-2, 23%). Although only XLP-1 patients developed lymphomas (30%), XLP-2 patients (17%) had chronic hemorrhagic colitis as documented by histopathology. Recurrent splenomegaly often associated with cytopenia and fever was preferentially observed in XLP-2 (XLP-1, 7%; XLP-2, 87%) and probably represents minimal forms of HLH as documented by histopathology. This first phenotypic comparison of XLP subtypes should help to improve the diagnosis and the care of patients with XLP conditions.
HLA-matched sibling bone marrow transplantation for β-thalassemia major
Authors: Sabloff Mitchell , Chandy Mammen , Wang Zhiwei , Logan Brent R. , Ghavamzadeh Ardeshir , Li Chi-Kong , Irfan Syed Mohammad , Bredeson Christopher N. , Cowan Morton J. , Gale Robert Peter , Hale Gregory A. , Horan John , Hongeng Suradej , Eapen Mary , Walters Mark C. 
Published: November 2010

Abstract
We describe outcomes after human leukocyte antigen-matched sibling bone marrow transplantation (BMT) for 179 patients with β-thalassemia major. The median age at transplantation was 7 years and the median follow-up was 6 years. The distribution of Pesaro risk class I, II, and III categories was 2%, 42%, and 36%, respectively. The day 30 cumulative incidence of neutrophil recovery and day 100 platelet recovery were 90% and 86%, respectively. Seventeen patients had graft failure, which was fatal in 11. Six of 9 patients with graft failure are alive after a second transplantation. The day 100 probability of acute graft-versus-host disease and 5-year probability of chronic graft-versus-host disease was 38% and 13%, respectively. The 5-year probabilities of overall- and disease-free survival were 91% and 88%, respectively, for patients with Pesaro risk class II, and 64% and 62%, respectively, for Pesaro risk class III. In multivariate analysis, mortality risks were higher in patients 7 years of age and older and those with hepatomegaly before BMT. The leading causes of death were interstitial pneumonitis (n = 7), hemorrhage (n = 8), and veno-occlusive disease (n = 6). Proceeding to BMT in children younger than 7 years before development of end-organ damage, particularly in the liver, should improve results after BMT for β-thalassemia major.
Symptom variability in patients with severe COPD: a pan-European cross-sectional study
Authors: Kessler R. , Partridge M.R. , Miravitlles M. , Cazzola M. , Vogelmeier C. , Leynaud D. , Ostinelli J. 
Published: November 2010

In between exacerbations, chronic obstructive pulmonary disease (COPD) is usually regarded as a stable condition, but there is increasing recognition of variability in this state. This cross-sectional study assessed patients' perception of symptom variability.Participants were outpatients >45 yrs old with COPD, current or ex-smokers, forced expiratory volume in 1 s (FEV1) <50% predicted, FEV1/forced vital capacity <0.7 and no exacerbation leading to therapeutic intervention in the previous 3 months. Patients' perceptions of COPD symptoms and their impact on daily life activities were recorded. Alterations in therapy use in response to COPD worsening were also recorded.COPD symptoms were experienced by 2,258 (92.5%) out of 2,441 patients during the 7 days before interview. Breathlessness was the most common symptom (72.5%). Daily and/or weekly symptom variability was reported by 62.7% of symptomatic patients; the morning was the worst time of day. Factors associated with perception of variability of breathlessness included younger age, symptom severity and recruitment to the study by general practitioners. The perception of variability was significantly different between European countries or regions.Patient-perceived COPD symptoms vary over the day and the week, and impact on daily activities; morning being the worst time of day. The majority of patients appear not to adjust treatment when symptoms worsen.
The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses
Authors: Pérez-Ruiz Alexander , Julià-Sapé Margarida , Mercadal Guillem , Olier Iván , Majós Carles , Arús Carles 
Published: November 2010

Abstract

Background
Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra of metabolites in the tissues. In pathological situations, the MRS profile changes and this has been particularly described for brain tumours. However, radiologists are frequently not familiar to the interpretation of MRS data and for this reason, the usefulness of decision-support systems (DSS) in MRS data analysis has been explored.

Results
This work presents the INTERPRET DSS version 3.0, analysing the improvements made from its first release in 2002. Version 3.0 is aimed to be a program that 1st, can be easily used with any new case from any MR scanner manufacturer and 2nd, improves the initial analysis capabilities of the first version. The main improvements are an embedded database, user accounts, more diagnostic discrimination capabilities and the possibility to analyse data acquired under additional data acquisition conditions. Other improvements include a customisable graphical user interface (GUI). Most diagnostic problems included have been addressed through a pattern-recognition based approach, in which classifiers based on linear discriminant analysis (LDA) were trained and tested.

Conclusions
The INTERPRET DSS 3.0 allows radiologists, medical physicists, biochemists or, generally speaking, any person with a minimum knowledge of what an MR spectrum is, to enter their own SV raw data, acquired at 1.5 T, and to analyse them. The system is expected to help in the categorisation of MR Spectra from abnormal brain masses.
Visceral regeneration in a sea cucumber involves extensive expression of survivin and mortalin homologs in the mesothelium
Authors: Mashanov Vladimir S , Zueva Olga R , Rojas-Catagena Carmencita , Garcia-Arraras Jose E 
Published: November 2010

Abstract
Background
The proper balance of cell division and cell death is of crucial importance for all kinds of developmental processes and for maintaining tissue homeostasis in mature tissues. Dysregulation of this balance often results in severe pathologies, such as cancer. There is a growing interest in understanding the factors that govern the interplay between cell death and proliferation under various conditions. Survivin and mortalin are genes that are known to be implicated in both mitosis and apoptosis and are often expressed in tumors.

Results
The present study takes advantage of the ability of the sea cucumber Holothuria glaberrima Selenka, 1867 (Holothuroidea, Aspidochirota) to discard its viscera and completely regrow them. This visceral regeneration involves an extensive expression of survivin and mortalin transcripts in the gut mesothelium (the outer tissue layer of the digestive tube), which coincides in time with drastic de-differentiation and a burst in cell division and apoptosis. Double labeling experiments (in situ hybridization combined with TUNEL assay or with BrdU immunohistochemistry) suggest that both genes support cell proliferation, while survivin might also be involved in suppression of the programmed cell death.

Conclusions
Visceral regeneration in the sea cucumber H. glaberrima is accompanied by elevated levels of cell division and cell death, and, moreover, involves expression of pro-cancer genes, such as survivin and mortalin, which are known to support proliferation and inhibit apoptosis. Nevertheless, once regeneration is completed and the expression pattern of both genes returns to normal, the regrown digestive tube shows no anomalies. This strongly suggests that sea cucumbers must possess some robust cancer-suppression mechanisms that allow rapid re-growth of the adult tissues without leading to runaway tumor development.
Comparative genomics of prevaccination and modern Bordetella pertussis strains
Authors: Bart Marieke J , van Gent Marjolein , van der Heide Han GJ , Boekhorst Jos , Hermans Peter , Parkhill Julian , Mooi Frits R 
Published: November 2010

Abstract

Background
Despite vaccination since the 1950s, pertussis has persisted and resurged. It remains a major cause of infant death worldwide and is the most prevalent vaccine-preventable disease in developed countries. The resurgence of pertussis has been associated with the expansion of Bordetella pertussis strains with a novel allele for the pertussis toxin (Ptx) promoter, ptxP3, which have replaced resident ptxP1 strains. Compared to ptxP1 strains, ptxP3 produce more Ptx resulting in increased virulence and immune suppression. To elucidate how B. pertussis has adapted to vaccination, we compared genome sequences of two ptxP3 strains with four strains isolated before and after the introduction vaccination.

Results
The distribution of SNPs in regions involved in transcription and translation suggested that changes in gene regulation play an important role in adaptation. No evidence was found for acquisition of novel genes. Modern strains differed significantly from prevaccination strains, both phylogenetically and with respect to particular alleles. The ptxP3 strains were found to have diverged recently from modern ptxP1 strains. Differences between ptxP3 and modern ptxP1 strains included SNPs in a number of pathogenicity-associated genes. Further, both gene inactivation and reactivation was observed in ptxP3 strains relative to modern ptxP1 strains.

Conclusions
Our work suggests that B. pertussis adapted by successive accumulation of SNPs and by gene (in)activation. In particular changes in gene regulation may have played a role in adaptation.
Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar
Authors: Pechanova Olga , Hsu Chuan-Yu , Adams Joshua P , Pechan Tibor , Vandervelde Lindsay , Drnevich Jenny , Jawdy Sara , Adeli Ardeshir , Suttle Jeffrey C , Lawrence Amanda M , Tschaplinski Timothy J , Séguin Armand , Yuceer Cetin 
Published: November 2010

AbstractBackgroundRiverine ecosystems, highly sensitive to climate change and human activities, are characterized by rapid environmental change to fluctuating water levels and siltation, causing stress on their biological components. We have little understanding of mechanisms by which riverine plant species have developed adaptive strategies to cope with stress in dynamic environments while maintaining growth and development.ResultsWe report that poplar (Populusspp.) has evolved a systems level "stress proteome" in the leaf-stem-root apoplast continuum to counter biotic and abiotic factors. To obtain apoplast proteins fromP. deltoides, we developed pressure-chamber and water-displacement methods for leaves and stems, respectively. Analyses of 303 proteins and corresponding transcripts coupled with controlled experiments and bioinformatics demonstrate that poplar depends on constitutive and inducible factors to deal with water, pathogen, and oxidative stress. However, each apoplast possessed a unique set of proteins, indicating that response to stress is partly compartmentalized. Apoplast proteins that are involved in glycolysis, fermentation, and catabolism of sucrose and starch appear to enable poplar to grow normally under water stress. Pathogenesis-related proteins mediating water and pathogen stress in apoplast were particularly abundant and effective in suppressing growth of the most prevalent poplar pathogenMelampsora. Unexpectedly, we found diverse peroxidases that appear to be involved in stress-induced cell wall modification in apoplast, particularly during the growing season. Poplar developed a robust antioxidative system to buffer oxidation in stem apoplast.ConclusionThese findings suggest that multistress response in the apoplast constitutes an important adaptive trait for poplar to inhabit dynamic environments and is also a potential mechanism in other riverine plant species.
High diversity of root associated fungi in both alpine and arctic Dryas octopetala
Authors: Bjorbækmo Marit Frederikke Markussen , Carlsen Tor , Brysting Anne , Vrålstad Trude , Høiland Klaus , Ugland Karl Inne , Geml Jozsef , Schumacher Trond , Kauserud Håvard 
Published: November 2010

Abstract

Background

Dryas octopetala is a widespread dwarf shrub in alpine and arctic regions that forms ectomycorrhizal (ECM) symbiotic relationships with fungi. In this study we investigated the fungal communities associated with roots of D. octopetala in alpine sites in Norway and in the High Arctic on Svalbard, where we aimed to reveal whether the fungal diversity and species composition varied across the Alpine and Arctic regions. The internal transcribed spacer (ITS) region of nuclear ribosomal DNA was used to identify the fungal communities from bulk root samples obtained from 24 plants.

Results
A total of 137 operational taxonomic units (OTUs) were detected (using 97% similarity cut off during sequence clustering) and well-known ECM genera such as Cenococcum, Cortinarius, Hebeloma, Inocybe and Tomentella occurred frequently. There was no decrease in fungal diversity with increasing latitude. The overall spatial heterogeneity was high, but a weak geographical structuring of the composition of OTUs in the root systems was observed. Calculated species accumulation curves did not level off.

Conclusions
This study indicates that the diversity of fungi associated with D. octopetala does not decrease in high latitude arctic regions, which contrasts observations made in a wide spectrum of other organism groups. A high degree of patchiness was observed across root systems, but the fungal communities were nevertheless weakly spatially structured. Non-asymptotical species accumulation curves and the occurrence of a high number of singletons indicated that only a small fraction of the fungal diversity was detected.
Genetic structure and ecogeographical adaptation in wild barley (Hordeum chilenseRoemer et Schultes) as revealed by microsatellite markers
Authors: Castillo Almudena , Dorado Gabriel , Feuillet Catherine , Sourdille Pierre , Hernandez Pilar 
Published: November 2010

AbstractBackgroundMulti-allelic microsatellite markers have become the markers of choice for the determination of genetic structure in plants. Synteny across cereals has allowed the cross-species and cross-genera transferability of SSR markers, which constitute a valuable and cost-effective tool for the genetic analysis and marker-assisted introgression of wild related species.Hordeum chilenseis one of the wild relatives with a high potential for cereal breeding, due to its high crossability (both interspecies and intergenera) and polymorphism for adaptation traits. In order to analyze the genetic structure and ecogeographical adaptation of this wild species, it is necessary to increase the number of polymorphic markers currently available for the species. In this work, the possibility of using syntenic wheat SSRs as a new source of markers for this purpose has been explored.ResultsFrom the 98 wheat EST-SSR markers tested for transferability and polymorphism in the wild barley genome, 53 primer pairs (54.0%) gave cross-species transferability and 20 primer pairs (20.4%) showed polymorphism. The latter were used for further analysis in theH. chilensegermplasm. TheH. chilense-Triticum aestivumaddition lines were used to test the chromosomal location of the new polymorphic microsatellite markers. The genetic structure and diversity was investigated in a collection of 94H. chilenseaccessions, using a set of 49 SSR markers distributed across the seven chromosomes. Microsatellite markers showed a total of 351 alleles over all loci. The number of alleles per locus ranged from two to 27, with a mean of 7.2 alleles per locus and a mean Polymorphic Information Content (PIC) of 0.5.ConclusionsAccording to the results, the germplasm can be divided into two groups, with morphological and ecophysiological characteristics being key determinants of the population structure. Geographic and ecological structuring was also revealed in the analyzed germplasm. A significant correlation between geographical and genetic distance was detected in the Central Chilean region for the first time in the species. In addition, significant ecological influence in genetic distance has been detected for one of the population structure groups (group II) in the Central Chilean region. Finally, the association of the SSR markers with ecogeographical variables was investigated and one marker was found significantly associated with precipitation. These findings have a potential application in cereal breeding.
Behavioural and psychological symptoms in the older population without dementia - relationship with socio-demographics, health and cognition
Authors: van der Linde Rianne , Stephan Blossom CM , Matthews Fiona E , Brayne Carol , Savva George M ,   the Medical Research Council Cognitive Function and Ageing Study
Published: November 2010

Abstract

Background
Behavioural and psychological symptoms are associated with dementia, but are also present in a significant number of the older population without dementia. Here we explore the distribution of behavioural and psychological symptoms in the population without dementia, and their relationship with domains and severity of health and cognitive impairment.

Methods
The Medical Research Council Cognitive Function and Ageing Study is a two-phase longitudinal study of ageing representative of the population aged 65 and over of England and Wales. A subsample of 1781 participants without a study diagnosis of dementia was included in this study. Information on symptoms including depression, apathy, anxiety, feelings of persecution, hallucination, agitated behaviour, elation, irritability, sleep problems, wandering, confabulation and misidentification, cognitive function, health related factors and socio-demographic information was extracted from interviews with participants and knowledgeable informants. Participants were classified according to the Mini-Mental State Examination and by criteria for subtypes of mild cognitive impairment (MCI). The prevalence of behavioural and psychological symptoms and associations with cognitive function, health and socio-demographics was examined. Co-occurrence of symptoms was tested using factor analysis.

Results
Most symptoms were reported more frequently in those with more severe cognitive impairment. Subjective memory complaints were the strongest independent predictor of reported symptoms, and most were reported more often in those classified as having MCI than in those with cognitive impairments that did not meet the MCI criteria. The pattern of co-occurrence of symptoms is similar to that seen in dementia.

Conclusions
Our results highlight that behavioural and psychological symptoms are prevalent in the cognitively impaired older population, and partly explain the variation observed in previous cohorts of individuals with MCI. Behavioural and psychological symptoms offer a target for intervention and so are an important consideration in the assessment of cognitively impaired older people.
High prevalence of germline STK11mutations in Hungarian Peutz-Jeghers Syndrome patients
Authors: Papp Janos , Kovacs Marietta Eva , Solyom Szilvia , Kasler Miklos , Børresen-Dale Anne-Lise , Olah Edith 
Published: November 2010

Abstract

Background
Peutz-Jeghers syndrome (PJS) is a rare autosomal dominantly inherited disease characterized by gastrointestinal hamartomatous polyposis and mucocutaneous pigmentation. The genetic predisposition for PJS has been shown to be associated with germline mutations in the STK11/LKB1 tumor suppressor gene. The aim of the present study was to characterize Hungarian PJS patients with respect to germline mutation in STK11/LKB1 and their association to disease phenotype.

Methods
Mutation screening of 21 patients from 13 PJS families were performed using direct DNA sequencing and multiplex ligation-dependent probe amplification (MLPA). Comparative semi-quantitative sequencing was applied to investigate the mRNA-level effects of nonsense and splice-affecting mutations.

Results
Thirteen different pathogenic mutations in STK11, including a high frequency of large genomic deletions (38%, 5/13), were identified in the 13 unrelated families studied. One of these deletions also affects two neighboring genes (SBNO2 and GPX4), located upstream of STK11, with a possible modifier effect. The majority of the point mutations (88%, 7/8) can be considered novel. Quantification of the STK11 transcript at the mRNA-level revealed that the expression of alleles carrying a nonsense or frameshift mutation was reduced to 30-70% of that of the wild type allele. Mutations affecting splice-sites around exon 2 displayed an mRNA processing pattern indicative of co-regulated splicing of exons 2 and 3.

Conclusions
A combination of sensitive techniques may assure a high (100%) STK11 mutation detection frequency in PJS families. Characterization of mutations at mRNA level may give a deeper insight into the molecular consequences of the pathogenic mutations than predictions made solely at the genomic level.