bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulmonary vascular disease in mice xenografted with human BM progenitors from patients with pulmonary arterial hypertension
Authors: Asosingh Kewal , Farha Samar , Lichtin Alan , Graham Brian , George Deepa , Aldred Micheala , Hazen Stanley L. , Loyd James , Tuder Rubin , Erzurum Serpil C. 
Published: June 2012

AbstractHematopoietic myeloid progenitors released into the circulation are able to promote vascular remodeling through endothelium activation and injury. Endothelial injury is central to the development of pulmonary arterial hypertension (PAH), a proliferative vasculopathy of the pulmonary circulation, but the origin of vascular injury is unknown. In the present study, mice transplanted with BM-derived CD133+ progenitor cells from patients with PAH, but not from healthy controls, exhibited morbidity and/or death due to features of PAH: in situ thrombi and endothelial injury, angioproliferative remodeling, and right ventricular hypertrophy and failure. Myeloid progenitors from patients with heritable and/or idiopathic PAH all produced disease in xenografted mice. Analyses of hematopoietic transcription factors and colony formation revealed underlying abnormalities of progenitors that skewed differentiation toward the myeloid-erythroid lineage. The results of the present study suggest a causal role for hematopoietic stem cell abnormalities in vascular injury, right ventricular hypertrophy, and morbidity associated with PAH.
Revised International Prognostic Scoring System for Myelodysplastic Syndromes
Authors: Greenberg Peter L. , Tuechler Heinz , Schanz Julie , Sanz Guillermo , Garcia-Manero Guillermo , Solé Francesc , Bennett John M. , Bowen David , Fenaux Pierre , Dreyfus Francois , Kantarjian Hagop , Kuendgen Andrea , Levis Alessandro , Malcovati Luca , Cazzola Mario , Cermak Jaroslav , Fonatsch Christa , Le Beau Michelle M. , Slovak Marilyn L. , Krieger Otto , Luebbert Michael , Maciejewski Jaroslaw , Magalhaes Silvia M. M. , Miyazaki Yasushi , Pfeilstöcker Michael , Sekeres Mikkael , Sperr Wolfgang R. , Stauder Reinhard , Tauro Sudhir , Valent Peter , Vallespi Teresa , van de Loosdrecht Arjan A. , Germing Ulrich , Haase Detlef 
Published: June 2012

AbstractThe International Prognostic Scoring Sytem (IPSS) is an important standard for ssessing prognosis of primary untreated adult patients with myelodysplastic syndromes (MDS). To refine the IPSS, MDS patient databases from international institutions were coalesced to assemble a much larger combined database (Revised-IPSS [IPSS-R], n = 7012, IPSS, n = 816) for analysis. Multiple statistically weighted clinical features were used to generate a prognostic categorization model. Bone marrow cytogenetics, marrow blast percentage, and cytopenias remained the basis of the new system. Novel components of the current analysis included: 5 rather than 3 cytogenetic prognostic subgroups with specific and new classifications of a number of less common cytogenetic subsets, splitting the low marrow blast percentage value, and depth of cytopenias. This model defined 5 rather than the 4 major prognostic categories that are present in the IPSS. Patient age, performance status, serum ferritin, and lactate dehydrogenase were significant additive features for survival but not for acute myeloid leukemia transformation. This system comprehensively integrated the numerous known clinical features into a method analyzing MDS patient prognosis more precisely than the initial IPSS. As such, this IPSS-R should prove beneficial for predicting the clinical outcomes of untreated MDS patients and aiding design and analysis of clinical trials in this disease.
Evolution of coding and non-coding genes in HOX clusters of a marsupial
Authors: Yu Hongshi , Lindsay James , Feng Zhi-Ping , Frankenberg Stephen , Hu Yanqiu , Carone Dawn , Shaw Geoff , Pask Andrew J , O’Neill Rachel , Papenfuss Anthony T , Renfree Marilyn B 
Published: June 2012

AbstractBackgroundThe HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals.ResultsHere we report a comparative analysis ofHOXgene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation ofHOXgene sequence and structure and non-protein coding genes including the microRNAsmiR-196a,miR-196b,miR-10aandmiR-10band the long non-coding RNAsHOTAIR,HOTAIRM1andHOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10aandmiR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such asmiR-10,miR-414andmiR-464, were found in the tammarHOXclusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammarHOXBandHOXDclusters.ConclusionsThis study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation ofHOXgenes to influence the body plan of this marsupial.
Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration
Authors: Nyberg Kevin G , Conte Matthew A , Kostyun Jamie L , Forde Alison , Bely Alexandra E 
Published: June 2012

Abstract

Background
The naid annelids contain a number of species that vary in their ability to regenerate lost body parts, making them excellent candidates for evolution of regeneration studies. However, scant sequence data exists to facilitate such studies. We constructed a cDNA library from the naid Pristina leidyi, a species that is highly regenerative and also reproduces asexually by fission, using material from a range of regeneration and fission stages for our library. We then sequenced the transcriptome of P. leidyi using 454 technology.

Results
454 sequencing produced 1,550,174 reads with an average read length of 376 nucleotides. Assembly of 454 sequence reads resulted in 64,522 isogroups and 46,679 singletons for a total of 111,201 unigenes in this transcriptome. We estimate that over 95% of the transcripts in our library are present in our transcriptome. 17.7% of isogroups had significant BLAST hits to the UniProt database and these include putative homologs of a number of genes relevant to regeneration research. Although many sequences are incomplete, the mean sequence length of transcripts (isotigs) is 707 nucleotides. Thus, many sequences are large enough to be immediately useful for downstream applications such as gene expression analyses. Using in situ hybridization, we show that two Wnt/β-catenin pathway genes (homologs of frizzled and β-catenin) present in our transcriptome are expressed in the regeneration blastema of P. leidyi, demonstrating the usefulness of this resource for regeneration research.

Conclusions
454 sequencing is a rapid and efficient approach for identifying large numbers of genes in an organism that lacks a sequenced genome. This transcriptome dataset will be a valuable resource for molecular analyses of regeneration in P. leidyi and will serve as a starting point for comparisons to non-regenerating naids. It also contributes significantly to the still limited genomic resources available for annelids and lophotrochozoans more generally.
Predicting cancer-associated germline variations in proteins
Authors: Martelli Pier Luigi , Fariselli Piero , Balzani Eva , Casadio Rita 
Published: June 2012

Abstract

Background
Various computational methods are presently available to classify whether a protein variation is disease-associated or not. However data derived from recent technological advancements make it feasible to extend the annotation of disease-associated variations in order to include specific phenotypes. Here we tackle the problem of distinguishing between genetic variations associated to cancer and variations associated to other genetic diseases.

Results
We implement a new method based on Support Vector Machines that takes as input the protein variant and the protein function, as described by its associated Gene Ontology terms. Our approach succeeds in discriminating between germline variants that are likely to be cancer-associated from those that are related to other genetic disorders. The method performs with values of 90% accuracy and 0.61 Matthews correlation coefficient on a set comprising 6478 germline variations (16% are cancer-associated) in 592 proteins. The sensitivity and the specificity on the cancer class are 69% and 66%, respectively. Furthermore the method is capable of correctly excluding some 96% of 3392 somatic cancer-associated variations in 1983 proteins not included in the training/testing set.

Conclusions
Here we prove feasible that a large set of cancer associated germline protein variations can be successfully discriminated from those associated to other genetic disorders. This is a step further in the process of protein variant annotation. Scoring largely improves when protein function as encoded by Gene Ontology terms is considered, corroborating the role of protein function as a key feature for a correct annotation of its variations.
Variation of chemosensory receptor content of Campylobacter jejuni strains and modulation of receptor gene expression under different in vivo and in vitro growth conditions
Authors: Day Christopher J , Hartley-Tassell Lauren E , Shewell Lucy K , King Rebecca M , Tram Greg , Day Serena K , Semchenko Evgeny A , Korolik Victoria 
Published: June 2012

Abstract

Background
Chemotaxis is crucial for the colonisation/infection of hosts with Campylobacter jejuni. Central to chemotaxis are the group A chemotaxis genes that are responsible for sensing the external environment. The distribution of group A chemoreceptor genes, as found in the C. jejuni sequenced strains, tlp1-4, 7, 10 and 11 were determined in 33 clinical human and avian isolates.

Results
Group A tlp gene content varied among the strains with genes encoding tlp1 (aspartate receptor, ccaA) and tlp7 present in all strains tested, where as tlp11 was present in only one of our international collection clinical isolates, C. jejuni 520, but was more prevalent (9/13) in the freshly isolated clinical stains from patients who required hospitalisation due to C. jejuni infection (GCH1-17). Relative expression levels of the group A tlp genes were also determined in C. jejuni reference strains NCTC 11168-GS, 11168-O and 81116 using cells grown in vitro at 37°C, 42°C and maintained at room temperature and with cells isolated directly from murine and avian hosts by immune magnetic separation without subsequent culture. Gene expression of tlp genes was varied based on strain, growth conditions and in vivo isolation source. Tlp1, although the most conserved, showed the lowest and most varied mRNA expression and protein production under laboratory conditions. Tlp7 was highly expressed at most conditions tested, and gene expression was not influenced by the tlp7 gene encoding a full length protein or one expressed as separate periplasmic and cytoplasmic domains.

Conclusion
We have shown that chemosensory receptor set variation exists among C. jejuni strains, but is not dependent on the isolation source.
Mediators between bereavement and somatic symptoms
Authors: Konkolÿ Thege Barna , Pilling János , Cserháti Zoltán , Koppˆ Maria S 
Published: June 2012

Abstract

Background
In our research we examined the frequency of somatic symptoms among bereaved (N = 185) and non-bereaved men and women in a national representative sample (N = 4041) and investigated the possible mediating factors between bereavement status and somatic symptoms.

Methods
Somatic symptoms were measured by the Patient Health Questionnaire (PHQ-15), anxiety with a four-point anxiety rating scale, and depression with a nine-item shortened version of the Beck Depression Inventory.

Results
Among the bereaved, somatic symptoms proved to be significantly more frequent in both genders when compared to the non-bereaved, as did anxiety and depression. On the multivariate level, the results show that both anxiety and depression proved to be a mediator between somatic symptoms and bereavement. The effect sizes indicated that for both genders, anxiety was a stronger predictor of somatic symptoms than depression.

Conclusions
The results of our research indicate that somatic symptoms accompanying bereavement are not direct consequences of this state but they can be traced back to the associated anxiety and depression. These results draw attention to the need to recognize anxiety and depression looming in the background of somatic complaints in bereavement and to the importance of the dissemination of related information.
The association between general practitioners’ attitudes towards breast cancer screening and women’s screening participation
Authors: Jensen Line Flytkjær , Mukai Thomas Ostersen , Andersen Berit , Vedsted Peter 
Published: June 2012

Abstract

Background
Breast cancer screening in Denmark is organised by the health services in the five regions. Although general practitioners (GPs) are not directly involved in the screening process, they are often the first point of contact to the health care system and thus play an important advisory role. No previous studies, in a health care setting like the Danish system, have investigated the association between GPs’ attitudes towards breast cancer screening and women’s participation in the screening programme.

Methods
Data on women’s screening participation was obtained from the regional screening authorities. Data on GPs’ attitudes towards breast cancer screening was taken from a previous survey among GPs in the Central Denmark Region. This study included women aged 50-69 years who were registered with a singlehanded GP who had participated in the survey.

Results
The survey involved 67 singlehanded GPs with a total of 13,288 women on their lists. Five GPs (7%) had a negative attitude towards breast cancer screening. Among registered women, 81% participated in the first screening round. Multivariate analyses revealed that women registered with a GP with a negative attitude towards breast cancer screening were 17% (95% CI: 2-34%) more likely to be non-participants compared with women registered with a GP with a positive attitude towards breast cancer screening.

Conclusion
The GPs' attitudes may influence the participation rate even in a system where GPs are not directly involved in the screening process. However, further studies are needed to investigate this association.
Change of water consumption and its potential influential factors in Shanghai: A cross-sectional study
Authors: Chen Hanyi , Zhang Yaying , Ma Linlin , Liu Fangmin , Zheng Weiwei , Shen Qinfeng , Zhang Hongmei , Wei Xiao , Tian Dajun , He Gengsheng , Qu Weidong 
Published: June 2012

Abstract

Background
Different water choices affect access to drinking water with different quality. Previous studies suggested social-economic status may affect the choice of domestic drinking water. The aim of this study is to investigate whether recent social economic changes in China affect residents’ drinking water choices.

Methods
We conducted a cross-sectional survey to investigate residents’ water consumption behaviour in 2011. Gender, age, education, personal income, housing condition, risk perception and personal preference of a certain type of water were selected as potential influential factors. Univariate and backward stepwise logistic regression analyses were performed to analyse the relation between these factors and different drinking water choices. Basic information was compared with that of a historical survey in the same place in 2001. Self-reported drinking-water-related diarrhoea was found correlated with different water choices and water hygiene treatment using chi-square test.

Results
The percentage of tap water consumption remained relatively stable and a preferred choice, with 58.99% in 2001 and 58.25% in 2011. The percentage of bottled/barrelled water consumption was 36.86% in 2001 and decreased to 25.75% in 2011. That of household filtrated water was 4.15% in 2001 and increased to 16.00% in 2011. Logistic regression model showed strong correlation between one’s health belief and drinking water choices (P < 0.001). Age, personal income, education, housing condition, risk perception also played important roles (P < 0.05) in the models. Drinking-water-related diarrhoea was found in all types of water and improper water hygiene behaviours still existed among residents.

Conclusions
Personal health belief, housing condition, age, personal income, education, taste and if worm ever founded in tap water affected domestic drinking water choices in Shanghai.
Parental reports of the oral health-related quality of life of children with cerebral palsy
Authors: Abanto Jenny , Carvalho Thiago S , Bönecker Marcelo , Ortega Adriana OL , Ciamponi Ana L , Raggio Daniela P 
Published: June 2012

Abstract

Background
The severity of physical and mental impairments and oral problems, as well as socioeconomic factors, may have an impact on quality of life of children with cerebral palsy (CP). The aim of this research was to assess the impact of impairments and oral health conditions, adjusted by socioeconomic factors, on the Oral Health-Related Quality of Life (OHRQoL) of children with CP using their parents as proxies.

Methods
Sixty children, between 6-14 years of age were selected. Their parents answered a children’s OHRQoL instrument (5 domains) which combines the Parental-Caregivers Perception Questionnaire (P-CPQ) and Family Impact Scale (FIS). The severity of dental caries, type of CP, communication ability, gross motor function, seizures and socioeconomic conditions were assessed.

Results
Considering the total score of the OHRQoL instrument, only the reduction of communication ability and dental caries severity had a negative impact on the OHRQoL (p < 0.05). Considering each domain of the instrument, the severity of the type of CP and its reduction of communication ability showed a negative impact on oral symptoms and functional limitations domains (p < 0.05). Seizures have a negative impact on oral symptoms domain (p = 0.006). The multivariate fitted model showed that the severity of dental caries, communication ability and low family income were negatively associated with the impact on OHRQoL (p = 0.001).

Conclusions
The severity of dental caries, communication ability, and family income are conditions strongly associated with a negative impact on OHRQoL of children with CP.
A randomized, double-blind comparison of OROS®hydromorphone and controlled-release morphine for the control of chronic cancer pain
Authors: Hanna Magdi , Thipphawong John ,   the 118 study group
Published: June 2012

Abstract

Background
Long-acting opioid formulations are advocated for maintaining pain control in chronic cancer pain. OROS® hydromorphone is a sustained-release formulation of hydromorphone that requires dosing once daily to maintain therapeutic concentrations. The objective of this study was to demonstrate the clinical equivalence of immediate-release and sustained-release formulations of hydromorphone and morphine for chronic cancer pain.

Methods
200 patients with cancer pain (requiring ≤ 540 mg/d of oral morphine) participated in this double-blind, parallel-group trial. Patients were randomized to receive hydromorphone or morphine (immediate-release for 2–9 days, sustained-release for 10–15 days). Efficacy was assessed with the Brief Pain Inventory (BPI), investigator and patient global evaluations, Eastern Cooperative Oncology Group performance status, and the Mini-Mental State Examination. The primary endpoint was the 'worst pain in the past 24 hours' item of the BPI, in both the immediate-release and sustained-release study phases, with treatments deemed equivalent if the 95% confidence intervals (CI) of the between-group differences at endpoint were between -1.5 and 1.5. No equivalence limits were defined for secondary endpoints.

Results
Least-squares mean differences (95% CI) between groups were 0.2 (-0.4, 0.9) in the immediate-release phase and -0.8 (-1.6, -0.01) in the sustained-release phase (intent-to-treat population), indicating that the immediate-release formulations met the pre-specified equivalence criteria, but that the lower limit of the 95% CI (-1.6) was outside the boundary (-1.5) for the sustained-release formulations. BPI 'pain now PM' was significantly lower with OROS® hydromorphone compared with controlled-release morphine (least-squares mean difference [95% CI], -0.77 [-1.49, -0.05]; p = 0.0372). Scores for other secondary efficacy variables were similar between the two sustained-release treatments. At endpoint, > 70% of investigators and patients rated both treatments as good to excellent. The safety profiles of hydromorphone and morphine were similar and typical of opioid analgesics.

Conclusion
Equivalence was demonstrated for immediate-release formulations of hydromorphone and morphine, but not for the sustained-release formulations of OROS® hydromorphone and controlled-release morphine. The direction of the mean difference between the treatments (-0.8) and the out-of-range lower limit of the 95% CI (-1.6) were in favor of OROS® hydromorphone.

Trial registration
ClinicalTrials.gov: NCT0041054