bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxidative stress in angiogenesis and vascular disease
Authors: Kim Young-Woong , Byzova Tatiana V. 
Published: December 2013

Abstract
Despite the damaging effect on tissues at a high concentration, it has been gradually established that oxidative stress plays a positive role during angiogenesis. In adults, physiological or pathological angiogenesis is initiated by tissue demands for oxygen and nutrients, resulting in a hypoxia/reoxygenation cycle, which, in turn promotes the formation of reactive oxygen species (ROS). The ROS can be generated either endogenously, through mitochondrial electron transport chain reactions and nicotinamide adenine dinucleotide phosphate oxidase, or exogenously, resulting from exposure to environmental agents, such as ultraviolet or ionizing radiation. In many conditions, ROS promotes angiogenesis, either directly or via the generation of active oxidation products, including peroxidized lipids. The latter lipid metabolites are generated in excess during atherosclerosis, thereby linking atherogenic processes and pathological angiogenesis. Although the main mechanism of oxidative stress-induced angiogenesis involves hypoxia-inducible factor/vascular endothelial growth factor (VEGF) signaling, recent studies have identified several pathways that are VEGF-independent. This review aims to provide a summary of the past and present views on the role of oxidative stress as a mediator and modulator of angiogenesis, and to highlight newly identified mechanisms.
MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis
Authors: Shivanandan Arun , Radenovic Aleksandra , Sbalzarini Ivo F 
Published: December 2013

Abstract

Background
Analyzing spatial distributions of objects in images is a fundamental task in many biological studies. The relative arrangement of a set of objects with respect to another set of objects contains information about potential interactions between the two sets of objects. If they do not “feel” each other’s presence, their spatial distributions are expected to be independent of one another. Spatial correlations in their distributions are indicative of interactions and can be modeled by an effective interaction potential acting between the points of the two sets. This can be used to generalize co-localization analysis to spatial interaction analysis. However, no user-friendly software for this type of analysis was available so far.

Results
We present an ImageJ/Fiji plugin that implements the complete workflow of spatial pattern and interaction analysis for spot-like objects. The plugin detects objects in images, infers the interaction potential that is most likely to explain the observed pattern, and provides statistical tests for whether an inferred interaction is significant given the number of objects detected in the images and the size of the space within which they can distribute. We benchmark and demonstrate the present software using examples from confocal and PALM single-molecule microscopy.

Conclusions
The present software greatly simplifies spatial interaction analysis for point patterns, and makes it available to the large user community of ImageJ and Fiji. The presented showcases illustrate the usage of the software.
Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters
Authors: Sibthorp Christopher , Wu Huihai , Cowley Gwendolyn , Wong Prudence W H , Palaima Paulius , Morozov Igor Y , Weedall Gareth D , Caddick Mark X 
Published: December 2013

Abstract

Background
The filamentous fungus Aspergillus nidulans has been a tractable model organism for cell biology and genetics for over 60 years. It is among a large number of Aspergilli whose genomes have been sequenced since 2005, including medically and industrially important species. In order to advance our knowledge of its biology and increase its utility as a genetic model by improving gene annotation we sequenced the transcriptome of A. nidulans with a focus on 5′ end analysis.

Results
Strand-specific whole transcriptome sequencing showed that 80-95% of annotated genes appear to be expressed across the conditions tested. We estimate that the total gene number should be increased by approximately 1000, to 11,800. With respect to splicing 8.3% of genes had multiple alternative transcripts, but alternative splicing by exon-skipping was very rare. 75% of annotated genes showed some level of antisense transcription and for one gene, meaB, we demonstrated the antisense transcript has a regulatory role. Specific sequencing of the 5’ ends of transcripts was used for genome wide mapping of transcription start sites, allowing us to interrogate over 7000 promoters and 5′ untranslated regions.

Conclusions
Our data has revealed the complexity of the A. nidulans transcriptome and contributed to improved genome annotation. The data can be viewed on the AspGD genome browser.
Chagas disease-specific antigens: characterization of epitopes in CRA/FRA by synthetic peptide mapping and evaluation by ELISA-peptide assay
Authors: Bottino Carolina G , Gomes Luciano P , Pereira José B , Coura José R , Provance David William , De-Simone Salvatore G 
Published: December 2013

Abstract

Background
The identification of epitopes in proteins recognized by medically relevant antibodies is useful for the development of peptide-based diagnostics and vaccines. In this study, epitopes in the cytoplasmic repetitive antigen (CRA) and flagellar repetitive antigen (FRA) proteins from Trypanosoma cruzi were identified using synthetic peptide techniques and pooled sera from Chagasic patients. The epitopes were further assayed with an ELISA assay based on synthetic peptides.

Methods
Twenty-two overlapping synthetic peptides representing the coding sequence of the T. cruzi CRA and FRA proteins were assessed by a Spot-synthesis array analysis using sera donated by patients with Chagas disease. Shorter peptides were selected that represented the determined epitopes and synthesized by solid phase synthesis to evaluate the patterns of cross-reactivities and discrimination through an ELISA-diagnostic assay.

Results
The peptide Spot-synthesis array successfully identified two IgG antigenic determinants in the CRA protein and four in FRA. Bioinformatics suggested that the CRA antigens were unique to T. cruzi while the FRA antigen showed similarity with sequences present within various proteins from Leishmania sp. Subsequently, shorter peptides representing the CRA-1, CRA-2 and FRA-1 epitopes were synthesized by solid phase synthesis and assayed by an ELISA-diagnostic assay. The CRA antigens gave a high discrimination between Chagasic, Leishmaniasis and T. cruzi-uninfected serum. A sensitivity and specificity of 100% was calculated for CRA. While the FRA antigen showed a slightly lower sensitivity (91.6%), its specificity was only 60%.

Conclusions
The epitopes recognized by human anti-T. cruzi antibodies have been precisely located in two biomarkers of T. cruzi, CRA and FRA. The results from screening a panel of patient sera through an ELISA assay based on peptides representing these epitopes strongly suggest that the sequences from CRA would be useful for the development of diagnostic reagents that could improve upon the sensitivity and specificity of currently available diagnostic tests. Overall, the results provide further evidence of the usefulness of identifying specific linear B-cell epitopes for improving diagnostic tools.
Is human immunodeficiency virus (HIV) stage an independent risk factor for altering the periodontal status of HIV-positive patients? A South African study
Authors: John Cathy Nisha , Stephen Lawrence Xavier , Joyce Africa Charlene Wilma 
Published: December 2013

Abstract

Background
The immunosuppresion in HIV patients makes them highly susceptible to microbial infections. The aim of the study was to establish whether HIV stage (as depicted by CD4+ T lymphocyte counts) could independently be associated with periodontal status (as revealed by the measurement of clinical indices).

Methods
One hundred and twenty HIV-infected patients attending an infectious diseases clinic in the Western Cape, South Africa were included in the study. The periodontal clinical indices such as plaque index, gingival index, pocket probing depth and clinical attachment levels were measured on the mesial aspect of the six Ramfjord teeth. The CD4 + T cell counts were taken from the patients’ medical records and patients’ HIV stage determined and grouped according to their CD4+ T cell counts into A (<200 cells /mm3), B (200–500 cells /mm3) and C (>500 cells /mm3).

Results
The mean age of 120 HIV-positive patients was 33.25 years and the mean CD4 + T cell count was 293.43 cells/mm3. The probing depth and clinical attachment loss were found to be significantly associated with the total CD4 + T cell counts but not with HIV stage. Significant correlations were found between age and all clinical indices except for clinical attachment loss. No correlation was found between age and HIV stage of the patients. The use of antiretroviral therapy was significantly associated with probing depth and clinical attachment loss, but not with plaque nor gingival index. Significant associations were observed between smoking and all of the clinical indices except for the gingival index. A significant association was observed between the use of interdental aids and all the clinical indices except for probing depth, while brushing was significantly associated with plaque index only. CD4 + T cell counts were significantly associated with brushing frequency (p = 0.0190) and the use of interdental aids (p = 0.0170).

Conclusion
The findings of this study conclude that HIV stage, ART and age are not independent risk factors for changes in the periodontal status of HIV-positive subjects but rather that smoking and oral hygiene habits determine their susceptibility to disease.
Segmentation of abdomen MR images using kernel graph cuts with shape priors
Authors: Luo Qing , Qin Wenjian , Wen Tiexiang , Gu Jia , Gaio Nikolas , Chen Shifu , Li Ling , Xie Yaoqin 
Published: December 2013

Abstract

Background
Abdominal organs segmentation of magnetic resonance (MR) images is an important but challenging task in medical image processing. Especially for abdominal tissues or organs, such as liver and kidney, MR imaging is a very difficult task due to the fact that MR images are affected by intensity inhomogeneity, weak boundary, noise and the presence of similar objects close to each other.

Method
In this study, a novel method for tissue or organ segmentation in abdomen MR imaging is proposed; this method combines kernel graph cuts (KGC) with shape priors. First, the region growing algorithm and morphology operations are used to obtain the initial contour. Second, shape priors are obtained by training the shape templates, which were collected from different human subjects with kernel principle component analysis (KPCA) after the registration between all the shape templates and the initial contour. Finally, a new model is constructed by integrating the shape priors into the kernel graph cuts energy function. The entire process aims to obtain an accurate image segmentation.

Results
The proposed segmentation method has been applied to abdominal organs MR images. The results showed that a satisfying segmentation without boundary leakage and segmentation incorrect can be obtained also in presence of similar tissues. Quantitative experiments were conducted for comparing the proposed segmentation with other three methods: DRLSE, initial erosion contour and KGC without shape priors. The comparison is based on two quantitative performance measurements: the probabilistic rand index (PRI) and the variation of information (VoI). The proposed method has the highest PRI value (0.9912, 0.9983 and 0.9980 for liver, right kidney and left kidney respectively) and the lowest VoI values (1.6193, 0.3205 and 0.3217 for liver, right kidney and left kidney respectively).

Conclusion
The proposed method can overcome boundary leakage. Moreover it can segment liver and kidneys in abdominal MR images without segmentation errors due to the presence of similar tissues. The shape priors based on KPCA was integrated into fully automatic graph cuts algorithm (KGC) to make the segmentation algorithm become more robust and accurate. Furthermore, if a shelter is placed onto the target boundary, the proposed method can still obtain satisfying segmentation results.
Proven invasive pulmonary mucormycosis successfully treated with amphotericin B and surgery in patient with acute myeloblastic leukemia: a case report
Authors: Vidovic Ana , Arsic-Arsenijevic Valentina , Tomin Dragica , Djunic Irena , Jakovic Radoslav , Loncar Zlatibor , Barac Aleksandra 
Published: December 2013

Abstract

Introduction
Invasive mucormycosis (zygomycosis) is the third most frequent fungal infection in patients with hematologic malignancies. It often results in a fatal outcome mainly due to the difficulty of early diagnosis and its resistance to antimycotics.

Case presentation
A 52-year-old Caucasian man was diagnosed with acute myeloblastic leukemia. Following the induction chemotherapy he developed febrile neutropenia. Meropenem (3×1000mg/day) was introduced empirically. A chest computed tomography showed soft-tissue consolidation change in his right upper lobe. A bronchoscopy was performed and the histology indicated invasive pulmonary aspergillosis based on fungal hypha detection. Also, high risk patients are routinely screened for invasive fungal infections using commercially available serological enzyme-linked immunosorbent assay tests: galactomannan and mannan (Bio-Rad, France), as well as anti-Aspergillus immunoglobulin G and/or immunoglobulin M and anti-Candida immunoglobulin G and/or immunoglobulin M antibodies (Virion-Serion, Germany). Galactomannan showed low positivity and voriconazole therapy (2×400mg/first day; 2×300mg/following days) was implemented. The patient became afebrile and a partial remission of disease was established. After 2 months, the patient developed a fever and a chest multi-slice computed tomography showed soft-tissue mass compressing his upper right bronchus. Voriconazole (2×400mg/first day; 2×300mg/following days) was reintroduced and bronchoscopy was repeated. Histologic examination of the new specimen was done, as well as a revision of the earlier samples in the reference laboratory and the diagnosis was switched to invasive pulmonary mucormycosis. The treatment was changed to amphotericin B colloidal dispersion (1×400mg/day). The complete remission of acute myeloblastic leukemia was verified after 2 months. During his immunerestitution, a high positivity of the anti-Aspergillus immunoglobulin M antibodies was found in a single serum sample and pulmonary radiography was unchanged. A lobectomy of his right upper pulmonary lobe was done and the mycology culture of the lung tissue sample revealed Rhizopus oryzae. He remained in complete remission for more than 1 year.

Conclusions
Invasive mucormycosis was successfully treated with amphotericin B, surgery and secondary itraconazole prophylaxis. As a rare disease invasive mucormycosis is not well understood by the medical community and therefore an improvement of education about prevention, diagnosis and treatment of invasive mucormycosis is necessary.
The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.)
Authors: Nicolè Silvia , Barcaccia Gianni , Erickson David L , Kress John W , Lucchin Margherita 
Published: December 2013

AbstractBackgroundVitis viniferaL. is one of society’s most important agricultural crops with a broad genetic variability. The difficulty in recognizing grapevine genotypes based on ampelographic traits and secondary metabolites prompted the development of molecular markers suitable for achieving variety genetic identification.FindingsHere, we propose a comparison between a multi-locus barcoding approach based on six chloroplast markers and a single-copy nuclear gene sequencing method using five coding regions combined with a character-based system with the aim of reconstructing cultivar-specific haplotypes and genotypes to be exploited for the molecular characterization of 157 V. viniferaaccessions. The analysis of the chloroplast target regions proved the inadequacy of the DNA barcoding approach at the subspecies level, and hence further DNA genotyping analyses were targeted on the sequences of five nuclear single-copy genes amplified across all of the accessions. The sequencing of the coding region of the UFGT nuclear gene (UDP-glucose: flavonoid 3-0-glucosyltransferase, the key enzyme for the accumulation of anthocyanins in berry skins) enabled the discovery of discriminant SNPs (1/34 bp) and the reconstruction of 130 V. viniferadistinct genotypes. Most of the genotypes proved to be cultivar-specific, and only few genotypes were shared by more, although strictly related, cultivars.ConclusionOn the whole, this technique was successful for inferring SNP-based genotypes of grapevine accessions suitable for assessing the genetic identity and ancestry of international cultivars and also useful for corroborating some hypotheses regarding the origin of local varieties, suggesting several issues of misidentification (synonymy/homonymy).
Synovial membrane immunohistology in early-untreated rheumatoid arthritis reveals high expression of catabolic bone markers that is modulated by methotrexate
Authors: Revu Shankar , Neregård Petra , af Klint Erik , Korotkova Marina , Catrina Anca Irinel 
Published: December 2013

Abstract
Introduction
We aimed to investigate the expression and therapeutic modulation of the receptor activator of the NF-κB ligand (RANKL) system in early-untreated rheumatoid arthritis (RA).

Methods
In this study, 15 patients with newly diagnosed RA (median symptom duration 7 months) were started on methotrexate (MTX) 20 mg weekly. Synovial biopsies were obtained by needle arthroscopy at baseline and 8 weeks after initiation of therapy. X-rays of the hands and feet were obtained at baseline and 1 year after diagnosis. Immunohistochemistry was performed to detect RANKL, receptor activator of nuclear factor-κB (RANK) and osteoprotegerin (OPG) in the synovial biopsies. The in vitro effect of MTX was tested on RA-derived primary fibroblasts and the osteoblasts-like osteosarcoma cell line (rtPCR, Western blot and ELISA) and in osteoclasts (tartrate-resistant acid phosphatase staining and dentine pit formation assay).

Results
MTX decreased synovial cellularity as well as RANK expression and the RANKL/OPG ratio. We confirmed this effect by a decrease of the mRNA and protein RANKL/OPG ratio in synovial-derived fibroblasts and osteoblasts-like tumoral cells exposed in vitro to methotrexate. Supernatants from MTX treated osteoblasts-like tumoral cells prevented pre-osteoclast formation in the absence of exogenous RANKL. Furthermore, MTX blocked osteoclastogenesis from peripheral blood mononuclear cells despite the presence of macrophage colony stimulating factor and RANKL, which indicates that MTX directly inhibits osteoclastogenesis.

Conclusions
The synovial membrane of early-untreated RA is characterized by a high RANKL/OPG ratio that can be reversed by methotrexate.
Molecular mechanisms regulating the synergism between IL-32γ and NOD for the activation of eosinophils
Authors: Wong Chun-Kwok , Dong Jie , Lam Christopher Wai-Kei 
Published: December 2013

AbstractIL-32 is a proinflammatory cytokine associated with infections, autoimmune diseases, and allergic asthma. In the present study, we elucidated the synergistic effect of IL-32γ and NOD ligand on the activation of human eosinophils, principal effector cells for allergic inflammation, and the underlying mechanisms. Specific IL-32-binding protein, PR3, was found to localize on the cell surface and in the cytoplasm of eosinophils. IL-32γ was more capable of activating eosinophils than its isotype variant IL-32α and exhibited synergistic effect with NOD1 ligand iE-DAP and NOD2 ligand MDP on the induction of allergic inflammation-related IL-1β, TNF-α, and chemokines CXCL8, CCL3, and CCL4 (P&lt;0.05). Moreover, IL-32γ and iE-DAP or MDP induced the significant up-regulation of the cell-surface expression of adhesion molecule CD18 and ICAM-1 on eosinophils. Synergism between IL-32γ and NOD ligands was dependent on the activation of intracellular caspase 1, ERKs, p38 MAPK, and NF-κB pathways in eosinophils. The further-enhanced CD18 and ICAM-1 expression and production of cytokines and chemokines were observed in eosinophils cocultured with human bronchial epithelial BEAS-2B cells. Furthermore, combined treatment of IL-32γ and NOD ligand could activate the release of eosinophil extracellular DNA traps, thereby implying the pathogen-defense mechanisms of eosinophils. Together, the above study provides pivotal immunological mechanisms by which bacterial infection-mediated activation of NOD1,2, together with IL-32γ, can synergize the activation of eosinophils interacting with bronchial epithelial cells.
The newly found functions of MTOC in immunological response
Authors: Kloc Malgorzata , Kubiak Jacek Z , Li Xian C , Ghobrial Rafik M 
Published: December 2013

ABSTRACTThe MTOCs are present in all eukaryotic cells. In animal somatic cells, the MTOC function is played by a centrosome, which contains centrioles and PCM. The traditional view is that the MTOC is responsible for the organization of microtubular structures (the intracellular network, cilia, and flagella) in interphase cells, and the formation of the mitotic and meiotic spindle apparatus which is required for the partitioning of chromosomes in dividing cells. Recent evidence suggests that MTOC also plays a key role in the engagement of molecular motors, directional transport of granules, and polarization of subcellular structures and molecules. All of these functions are crucial for targeted cytotoxicity and the regulation of immune cells. In this review, we focus on the ultrastructural and molecular aspects of MTOCs in various aspects of immune cell functions, with specific emphasis on the formation of the IS and targeted cell killing.