bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Term Heart Transplant Survival by Targeting the Ionotropic Purinergic Receptor P2X7
Authors: Vergani Andrea , Tezza Sara , D’Addio Francesca , Fotino Carmen , Liu Kaifeng , Niewczas Monika , Bassi Roberto , Molano R. Damaris , Kleffel Sonja , Petrelli Alessandra , Soleti Antonio , Ammirati Enrico , Frigerio Maria , Visner Gary , Grassi Fabio , Ferrero Maria E. , Corradi Domenico , Abdi Reza , Ricordi Camillo , Sayegh Mohamed H. , Pileggi Antonello , Fiorina Paolo 
Published: December 2012

Background—
Heart transplantation is a lifesaving procedure for patients with end-stage heart failure. Despite much effort and advances in the field, current immunosuppressive regimens are still associated with poor long-term cardiac allograft outcomes, and with the development of complications, including infections and malignancies, as well. The development of a novel, short-term, and effective immunomodulatory protocol will thus be an important achievement. The purine ATP, released during cell damage/activation, is sensed by the ionotropic purinergic receptor P2X7 (P2X7R) on lymphocytes and regulates T-cell activation. Novel clinical-grade P2X7R inhibitors are available, rendering the targeting of P2X7R a potential therapy in cardiac transplantation.

Methods and Results—
We analyzed P2X7R expression in patients and mice and P2X7R targeting in murine recipients in the context of cardiac transplantation. Our data demonstrate that P2X7R is specifically upregulated in graft-infiltrating lymphocytes in cardiac-transplanted humans and mice. Short-term P2X7R targeting with periodate-oxidized ATP promotes long-term cardiac transplant survival in 80% of murine recipients of a fully mismatched allograft. Long-term survival of cardiac transplants was associated with reduced T-cell activation, T-helper cell 1/T-helper cell 17 differentiation, and inhibition of STAT3 phosphorylation in T cells, thus leading to a reduced transplant infiltrate and coronaropathy. In vitro genetic upregulation of the P2X7R pathway was also shown to stimulate T-helper cell 1/T-helper cell 17 cell generation. Finally, P2X7R targeting halted the progression of coronaropathy in a murine model of chronic rejection as well.

Conclusions—
P2X7R targeting is a novel clinically relevant strategy to prolong cardiac transplant survival.
Measurement Methods Affect the Observed Global Dimming and Brightening
Authors: Wang Kaicun , Dickinson Robert E. , Ma Qian , Augustine John A. , Wild Martin 
Published: December 2012

Abstract
Surface incident solar radiation G determines our climate and environment, and has been widely observed with a single pyranometer since the late 1950s. Such observations have suggested a widespread decrease between the 1950s and 1980s (global dimming), that is, at a rate of −3.5 W m−2 decade−1 (or −2% decade−1) from 1960 to 1990. Since the early 1990s, the diffuse and direct components of G have been measured independently, and a more accurate G has been calculated by summing these two measurements. Data from this summation method suggest that G increased at a rate of 6.6 W m−2 decade−1 (3.6% decade−1) from 1992 to 2002 (brightening) at selected sites. The brightening rates from these studies were also higher than those from a single pyranometer. In this paper, the authors used 17 years (1995–2011) of parallel measurements by the two methods from nearly 50 stations to test whether these two measurement methods of G provide similar long-term trends. The results show that although measurements of G by the two methods agree very well on a monthly time scale, the long-term trend from 1995 to 2011 determined by the single pyranometer is 2–4 W m−2 decade−1 less than that from the summation method. This difference of trends in the observed G is statistically significant. The dependence of trends of G on measurement methods uncovered here has an important implication for the widely reported global dimming and brightening based on datasets collected by different measurement methods; that is, the dimming might have been less if measured with current summation methods.
Routine Health Screening
Authors: Paepe Dominique , Verjans Gaëlle , Duchateau Luc , Piron Koen , Ghys Liesbeth , Daminet Sylvie 
Published: December 2012

Study rationale: Veterinary practitioners often perform geriatric health screening in cats. Unfortunately, scientific information regarding clinical and laboratory abnormalities and normal blood pressure values in elderly cats is scarce. This prospective study evaluated routine health screening tests in apparently healthy middle-aged and old cats. Protocol: One hundred cats of 6 years and older underwent blood pressure measurement, physical examination, blood and urine analysis, indirect fundoscopy and bilateral Schirmer tear tests. Findings: Mean systolic blood pressure (SBP) was 133.6 ± 21.5 mmHg. Increased SBP (>160 mmHg) was observed in eight cats, submandibular lymphadenopathy in 32, gingivitis in 72, heart murmur in 11, thyroid goitre in 20, increased creatinine in 29, hyperglycaemia in 25, increased total thyroxine in three, feline immunodeficiency virus positivity in 14, crystalluria in 41, borderline proteinuria in 25 and overt proteinuria in two. Mean tear production was very similar for both eyes and none of the cats had ocular lesions secondary to hypertension. Clinical significance: Old cats (>10 years) had significantly higher SBP, heart rate, murmur frequency, thrombocyte count, urine protein:creatinine ratio and serum urea and bilirubin concentrations, and significantly lower body condition score, haematocrit, albumin and total calcium concentrations than middle-aged cats (6–10 years). The common occurrence of physical examination and laboratory abnormalities in apparently healthy old cats underlines the need for regular health checks and the development of age-dependent laboratory reference intervals.
TIGER: tiled iterative genome assembler
Authors: Wu Xiao-Long , Heo Yun , El Hajj Izzat , Hwu Wen-Mei , Chen Deming , Ma Jian 
Published: December 2012

Abstract

Background
With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human diseases. De novo genome assembly is one of the most important steps to reconstruct the sequenced genome. However, most de novo assemblers require enormous amount of computational resource, which is not accessible for most research groups and medical personnel.

Results
We have developed a novel de novo assembly framework, called Tiger, which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems. Our method is also flexible to embed different assemblers for various types of target genomes. Using the sequence data from a human chromosome, our results show that Tiger can achieve much better NG50s, better genome coverage, and slightly higher errors, as compared to Velvet and SOAPdenovo, using modest amount of memory that are available in commodity computers today.

Conclusions
Most state-of-the-art assemblers that can achieve relatively high assembly quality need excessive amount of computing resource (in particular, memory) that is not available to most researchers to achieve high quality results. Tiger provides the only known viable path to utilize NGS de novo assemblers that require more memory than that is present in available computers. Evaluation results demonstrate the feasibility of getting better quality results with low memory footprint and the scalability of using distributed commodity computers.
Identification of five B-type response regulators as members of a multistep phosphorelay system interacting with histidine-containing phosphotransfer partners of Populus osmosensor
Authors: Bertheau Lucie , Chefdor Françoise , Guirimand Grégory , Courdavault Vincent , Depierreux Christiane , Morabito Domenico , Brignolas Franck , Héricourt François , Carpin Sabine 
Published: December 2012

Abstract

Background
In plants, the multistep phosphorelay signaling pathway mediates responses to environmental factors and plant hormones. This system is composed of three successive partners: hybrid Histidine-aspartate Kinases (HKs), Histidine-containing Phosphotransfer proteins (HPts), and Response Regulators (RRs). Among the third partners, B-type RR family members are the final output elements of the pathway; they act as transcription factors and clearly play a pivotal role in the early response to cytokinin in Arabidopsis. While interactions studies between partners belonging to the multistep phosphorelay system are mainly focused on protagonists involved in cytokinin or ethylene pathways, very few reports are available concerning partners of osmotic stress signaling pathway.

Results
In Populus, we identified eight B-type RR proteins, RR12-16, 19, 21 and 22 in the Dorskamp genotype. To assess HPt/B-type RR interactions and consequently determine potential third partners in the osmosensing multistep phosphorelay system, we performed global yeast two-hybrid (Y2H) assays in combination with Bimolecular Fluorescence Complementation (BiFC) assays in plant cells. We found that all B-type RRs are able to interact with HPt predominant partners (HPt2, 7 and 9) of HK1, which is putatively involved in the osmosensing pathway. However, different profiles of interaction are observed depending on the studied HPt. HPt/RR interactions displayed a nuclear localization, while the nuclear and cytosolic localization of HPt and nuclear localization of RR proteins were validated. Although the nuclear localization of HPt/RR interaction was expected, this work constitutes the first evidence of such an interaction in plants. Furthermore, the pertinence of this partnership is reinforced by highlighting a co-expression of B-type RR transcripts and the other partners (HK1 and HPts) belonging to a potential osmosensing pathway.

Conclusion
Based on the interaction studies between identified B-type RR and HPt proteins, and the co-expression analysis of transcripts of these potential partners in poplar organs, our results favor the model that RR12, 13, 14, 16 and 19 are able to interact with the main partners of HK1, HPt2, 7 and 9, and this HPt/RR interaction occurs within the nucleus. On the whole, the five B-type RRs of interest could be third protagonists putatively involved in the osmosensing signaling pathway in Populus.
Info-gap management of public health Policy for TB with HIV-prevalence and epidemiological uncertainty
Authors: Ben-Haim Yakov , Dacso Clifford C , Zetola Nicola M 
Published: December 2012

Abstract

Background
Formulation and evaluation of public health policy commonly employs science-based mathematical models. For instance, epidemiological dynamics of TB is dominated, in general, by flow between actively and latently infected populations. Thus modelling is central in planning public health intervention. However, models are highly uncertain because they are based on observations that are geographically and temporally distinct from the population to which they are applied.

Aims
We aim to demonstrate the advantages of info-gap theory, a non-probabilistic approach to severe uncertainty when worst cases cannot be reliably identified and probability distributions are unreliable or unavailable. Info-gap is applied here to mathematical modelling of epidemics and analysis of public health decision-making.

Methods
Applying info-gap robustness analysis to tuberculosis/HIV (TB/HIV) epidemics, we illustrate the critical role of incorporating uncertainty in formulating recommendations for interventions. Robustness is assessed as the magnitude of uncertainty that can be tolerated by a given intervention. We illustrate the methodology by exploring interventions that alter the rates of diagnosis, cure, relapse and HIV infection.

Results
We demonstrate several policy implications. Equivalence among alternative rates of diagnosis and relapse are identified. The impact of initial TB and HIV prevalence on the robustness to uncertainty is quantified. In some configurations, increased aggressiveness of intervention improves the predicted outcome but also reduces the robustness to uncertainty. Similarly, predicted outcomes may be better at larger target times, but may also be more vulnerable to model error.

Conclusions
The info-gap framework is useful for managing model uncertainty and is attractive when uncertainties on model parameters are extreme. When a public health model underlies guidelines, info-gap decision theory provides valuable insight into the confidence of achieving agreed-upon goals.
Effects of local phenytoin on seroma formation after mastectomy and Axillary lymph node dissection: an experimental study on mice
Authors: Eser Mehmet , Tutal Fırat , Kement Metin , Goktas Selcuk , Kaptanoglu Levent , Gökceimam Mehmet , Gecer Melin Ozgun , Uzun Huseyin 
Published: December 2012

Abstract

Background
Seroma formation is the most common complication after breast cancer surgery. It is an important complication since it prolongs therapy duration, increases cost, and negatively affects patient psychology. Currently, there is no widely accepted method that prevents seroma formation. We tried to investigate impact of local phenytoin application on seroma formation following an experimental mastectomy model created in rats.

Methods
Two groups including eight rats in each were randomized. Saline injection was applied in the first group, whereas 1% phenytoin was locally used in the second group. Ten days after the surgery, seroma formation and wound-healing processes were evaluated using histopathological and biochemical examinations.

Results
Phenytoin significantly decreased seroma formation. Fibrosis was significantly increased and angiogenesis was significantly reduced in the phenytoin group (P < 0.05). Increased levels of macrophage and lymphocyte infiltration was detected in the control group (P < 0.05). No difference was detected between the groups in terms of necrosis, edema, congestion, and PNL (Polymorphonuclear leucocyte) and fibroblast infiltration.

Conclusions
Seroma formation-reducing effect of phenytoin might have occurred over its anti-inflammatory, anti-angiogenetic, and fibrosis augmenting effects.
Mining biomarker information in biomedical literature
Authors: Younesi Erfan , Toldo Luca , Müller Bernd , Friedrich Christoph M , Novac Natalia , Scheer Alexander , Hofmann-Apitius Martin , Fluck Juliane 
Published: December 2012

Abstract

Background
For selection and evaluation of potential biomarkers, inclusion of already published information is of utmost importance. In spite of significant advancements in text- and data-mining techniques, the vast knowledge space of biomarkers in biomedical text has remained unexplored. Existing named entity recognition approaches are not sufficiently selective for the retrieval of biomarker information from the literature. The purpose of this study was to identify textual features that enhance the effectiveness of biomarker information retrieval for different indication areas and diverse end user perspectives.

Methods
A biomarker terminology was created and further organized into six concept classes. Performance of this terminology was optimized towards balanced selectivity and specificity. The information retrieval performance using the biomarker terminology was evaluated based on various combinations of the terminology's six classes. Further validation of these results was performed on two independent corpora representing two different neurodegenerative diseases.

Results
The current state of the biomarker terminology contains 119 entity classes supported by 1890 different synonyms. The result of information retrieval shows improved retrieval rate of informative abstracts, which is achieved by including clinical management terms and evidence of gene/protein alterations (e.g. gene/protein expression status or certain polymorphisms) in combination with disease and gene name recognition. When additional filtering through other classes (e.g. diagnostic or prognostic methods) is applied, the typical high number of unspecific search results is significantly reduced. The evaluation results suggest that this approach enables the automated identification of biomarker information in the literature. A demo version of the search engine SCAIView, including the biomarker retrieval, is made available to the public through http://www.scaiview.com/scaiview-academia.html.

Conclusions
The approach presented in this paper demonstrates that using a dedicated biomarker terminology for automated analysis of the scientific literature maybe helpful as an aid to finding biomarker information in text. Successful extraction of candidate biomarkers information from published resources can be considered as the first step towards developing novel hypotheses. These hypotheses will be valuable for the early decision-making in the drug discovery and development process.
Computer-aided diagnosis of breast microcalcifications based on dual-tree complex wavelet transform
Authors: Jian Wushuai , Sun Xueyan , Luo Shuqian 
Published: December 2012

Abstract

Background
Digital mammography is the most reliable imaging modality for breast carcinoma diagnosis and breast micro-calcifications is regarded as one of the most important signs on imaging diagnosis. In this paper, a computer-aided diagnosis (CAD) system is presented for breast micro-calcifications based on dual-tree complex wavelet transform (DT-CWT) to facilitate radiologists like double reading.

Methods
Firstly, 25 abnormal ROIs were extracted according to the center and diameter of the lesions manually and 25 normal ROIs were selected randomly. Then micro-calcifications were segmented by combining space and frequency domain techniques. We extracted three texture features based on wavelet (Haar, DB4, DT-CWT) transform. Totally 14 descriptors were introduced to define the characteristics of the suspicious micro-calcifications. Principal Component Analysis (PCA) was used to transform these descriptors to a compact and efficient vector expression. Support Vector Machine (SVM) classifier was used to classify potential micro-calcifications. Finally, we used the receiver operating characteristic (ROC) curve and free-response operating characteristic (FROC) curve to evaluate the performance of the CAD system.

Results
The results of SVM classifications based on different wavelets shows DT-CWT has a better performance. Compared with other results, DT-CWT method achieved an accuracy of 96% and 100% for the classification of normal and abnormal ROIs, and the classification of benign and malignant micro-calcifications respectively. In FROC analysis, our CAD system for clinical dataset detection achieved a sensitivity of 83.5% at a false positive per image of 1.85.

Conclusions
Compared with general wavelets, DT-CWT could describe the features more effectively, and our CAD system had a competitive performance.
Spontaneous arthritis and ankylosis in male DBA/1 mice: further evidence for a role of behavioral factors in “stress-induced arthritis”
Authors: Braem Kirsten , Carter Shea , Lories Rik J 
Published: December 2012

Abstract

Background
Ageing male DBA/1 mice spontaneously develop arthritis in the hind paws. We and others have demonstrated that this model shares striking features with human spondyloarthritis, in particular entheseal involvement, progressive ankylosis but also dactylitis. Here, we report on our recent experience with this model highlighting how changes in the animal facility affect the development of the disease.

Findings
Ageing male DBA/1 mice from different litters were caged together (6 mice per cage) at the age of 10 weeks. The mice were checked twice a week for clinical signs of arthritis. Disease severity was assessed in further detail post-mortem by scoring for histomorphological characteristics. DBA/1 mice spontaneously develop macroscopically detectable arthritis, presenting as joint swelling or toe stiffness. Standard settings with open cages lead to an almost 100% incidence by the age of 26 weeks. The introduction of larger cages and filter tops reducing exposure to other cages dramatically affected incidence. Other negative factors include excess bedding material reducing the impact of walking and running. Switching back to the original conditions resulted again in a high incidence, further optimized by sensory exposure to female mice. We also showed that the related DBA/2 strain is sensitive to the disease.

Conclusions
Changing environmental factors in the housing conditions of DBA/1 mice severely affects the spontaneous development of arthritis. This points out that the model is very sensitive to external stress and sensory factors that are likely affecting the behavior of the male mice and that the model needs to be optimized in different situations.
Hyaluronan production and chondrogenic properties of primary human chondrocyte on gelatin based hematostatic spongostan scaffold
Authors: Klangjorhor Jeerawan , Nimkingratana Puwapong , Settakorn Jongkolnee , Pruksakorn Dumnoensun , Leerapun Taninnit , Arpornchayanon Olarn , Rojanasthien Sattaya , Kongtawelert Prachya , Pothacharoen Peraphan 
Published: December 2012

Abstract

Background
Autologous chondrocyte transplantation is a promising technique for treatment of cartilage defects. Three dimensional chondrocyte cultures on a scaffold are widely used to retain the chondrogenic phenotype. Using a biodegradable gelatin scaffold is one option for the cell delivery system, but molecular and histological studies of the method have not yet been done.

Methods
We evaluated the chondrogenic property of the primary human chondrocyte on a gelatin scaffold as compared to a collagen scaffold over a period of 21 days. We examined the production of glycosaminoglycan by quantitative and histological analysis. Gene expression of cartilage-associated molecules was assessed by quantitative RT-PCR.

Results
The gelatin scaffold showed the ability to promote chondrocyte expansion, chondrogenic phenotype retention at molecular and mRNA levels.

Conclusions
This scaffold is thus suitable for use as an in vitro model for chondrocyte 3D culture.
Exploring the temporal development of childhood IgE profiles to allergen components
Authors: Önell Annica , Hjälle Lisbeth , Borres Magnus P 
Published: December 2012

AbstractBackgroundChildren often develop allergies that may or not persist into adulthood. Although the different allergic symptoms over time have been well documented, the underlying pattern of sensitization to various proteins and subsequent allergy development is unexplored.The aim was to study the sensitization pattern to allergen components over time from infancy to adulthood in a group of infants with heredity for allergic diseases.MethodsIgE profiles were monitored in a group of 67 children from 6 months to 18 years using a microarray chip (ImmunoCAP® ISAC) containing 103 allergen components derived from 47 allergen sources. The chip IgE profile was compared with clinical history, skin prick test results and diagnoses (atopic dermatitis, asthma and allergic rhinoconjunctivitis) at each time point for each child.ResultsIgE profiles were unique for each child and showed broad agreement with the results of skin prick tests and doctors’ diagnoses. In addition, close examination of the IgE profiles often revealed early indication of subsequent allergies. IgE profiles also facilitated the examination of cross‐reactivity contra co‐sensitization, thereby greatly enhancing the possibility for managing patients.ConclusionThis explorative description indicates that sensitization pattern to allergen components differs over time as well as among allergic individuals when examined with microarray technology.