bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unique clinicopathological features of metaplastic breast carcinoma compared with invasive ductal carcinoma and poor prognostic indicators
Authors: Song Yanni , Liu Xiaolong , Zhang Guoqiang , Song Hongtao , Ren Yanlv , He Xiaoguang , Wang Yanbo , Zhang Jinfeng , Zhang Youxue , Sun Shanshan , Liang Xiaoshuan , Sun Qian , Pang Da 
Published: June 2013

Abstract

Background
Metaplastic breast carcinoma is a rare aggressive malignant neoplasm. The purposes of this study are to review the pathologic features and clinical outcomes of metaplastic breast carcinoma compared to invasive ductal carcinoma and to evaluate the prognosis of metaplastic breast carcinoma.

Methods
The cases of 55 patients with metaplastic breast carcinomapresenting between 1991 and 2006 were analyzed and compared to the cases of 767 age-matched patients with invasive ductal carcinoma from the same time period.

Results
The group of patients with metaplastic breast carcinoma presented with a larger tumor size, lower lymph node involvement, higher percentage of triple-negative (estrogen receptor-, progesterone receptor- and human epidermal growth factor receptor-2-negative) cases, and Ki-67 over-expression compared with the group of patients with invasive ductal carcinoma and triple-negative invasive ductal carcinomas. Patients in the metaplastic breast carcinoma group tended to have more local (often chest wall) recurrences (P = 0.038) and distant (often lung) metastases (P = 0.001) than those in the invasive ductal carcinomas group. The prognosis of metaplastic breast carcinoma was poorer than that of invasive ductal carcinoma and triple-negative invasive ductal carcinomas; the 5-year overall survival rate was 54.5% in metaplastic breast carcinoma versus 85.1% in invasive ductal carcinoma, and 73.3% in triple-negative invasive ductal carcinomas (P <0.001). The 5-year disease-free survival rate was 45.5% in metaplastic breast carcinoma versus 71.2% in invasive ductal carcinoma, and 60.3% in triple-negative invasive ductal carcinomas (P <0.001). Multivariate analysis revealed tumor size larger than 5.0 cm, lymph node involvement and Ki-67≥14% were significantly related to 5-year overall survival (P = 0.010; P = 0.010; P = 0.035) and 5-year disease-free survival (P = 0.020; P = 0.018; P = 0.049).

Conclusions
Metaplastic breast carcinoma shows a poorer prognosis than both invasive ductal carcinoma and triple-negative invasive ductal carcinomas. Tumor size larger than 5.0 cm, lymph node involvement and Ki-67 ≥14% indicate a poor prognosis in patients with metaplastic breast carcinoma.
Iterative algorithms with errors for zero points of m-accretive operators
Authors: Qin Xiaolong , Cho Sun Young , Wang Lin 
Published: June 2013

Abstract
In this paper, we study the convergence of paths for continuous pseudocontractions in a real Banach space. As an application, we consider the problem of finding zeros of m-accretive operators based on an iterative algorithm with errors. Strong convergence theorems for zeros of m-accretive operators are established in a real Banach space.

MSC:47H05, 47H09, 47J25, 65J15.
Sequencing viral genomes from a single isolated plaque
Authors: DePew Jessica , Zhou Bin , McCorrison Jamison M , Wentworth David E , Purushe Janaki , Koroleva Galina , Fouts Derrick E 
Published: June 2013

Abstract

Background
Whole genome sequencing of viruses and bacteriophages is often hindered because of the need for large quantities of genomic material. A method is described that combines single plaque sequencing with an optimization of Sequence Independent Single Primer Amplification (SISPA). This method can be used for de novo whole genome next-generation sequencing of any cultivable virus without the need for large-scale production of viral stocks or viral purification using centrifugal techniques.

Methods
A single viral plaque of a variant of the 2009 pandemic H1N1 human Influenza A virus was isolated and amplified using the optimized SISPA protocol. The sensitivity of the SISPA protocol presented here was tested with bacteriophage F_HA0480sp/Pa1651 DNA. The amplified products were sequenced with 454 and Illumina HiSeq platforms. Mapping and de novo assemblies were performed to analyze the quality of data produced from this optimized method.

Results
Analysis of the sequence data demonstrated that from a single viral plaque of Influenza A, a mapping assembly with 3590-fold average coverage representing 100% of the genome could be produced. The de novo assembled data produced contigs with 30-fold average sequence coverage, representing 96.5% of the genome. Using only 10 pg of starting DNA from bacteriophage F_HA0480sp/Pa1651 in the SISPA protocol resulted in sequencing data that gave a mapping assembly with 3488-fold average sequence coverage, representing 99.9% of the reference and a de novo assembly with 45-fold average sequence coverage, representing 98.1% of the genome.

Conclusions
The optimized SISPA protocol presented here produces amplified product that when sequenced will give high quality data that can be used for de novo assembly. The protocol requires only a single viral plaque or as little as 10 pg of DNA template, which will facilitate rapid identification of viruses during an outbreak and viruses that are difficult to propagate.
Prevalence and type distribution of high-risk human papillomavirus in patients with cervical cancer: a population-based study
Authors: Haghshenas Mohammadreza , Golini-moghaddam Tahereh , Rafiei Alireza , Emadeian Omid , Shykhpour Ahmad , Ashrafi G Hossein 
Published: June 2013

Abstract

Background
Cervical cancer is the greater cause of cancer death in women in many developing countries. Persistent infection with human papilloma virus (HPV), primarily high risk types 16 and 18, is recognized as a causal and essential factor for the development of cervical cancer. We aimed to determine the distribution of high-risk HPV genotypes in archival biopsies with cervical carcinoma in patients from Mazandaran Province, Northern Iran.

Methods
A total of 98 paraffin-embedded cervical samples consisted of 63 Squamous Cell Carcinomas (SCC), 4 Adenocarcinomas, 19 Cervical Interaepithelial Neoplasia grade I (CIN-I), 4 CIN-II and 8 CIN-III diagnosed during 2009–2011, were selected to perform high risk HPV genotyping using AmpliSens(R) HPV HCR DNA genotyping kit. The prevalence of HPV infections was assessed in low and high grade cervical lesions by age.

Results
Of the 98 cervical samples analysed by DNA PCR, 78 (79.59%) were positive for HPV DNA. HPV was detected in the 52 of SCC, 4 of Adenocarcinomas, 14 of CIN-I, 4 of CIN-II, and 4 of CIN-III for HPV. From the 78 HPV positive samples, 23 (29.5%) samples were positive for HPV type 16, 32 (41%) were positive for HPV 18, 19 (24.4%) were positive for HPV 45, and 4 (5.1%) of cervical specimens were positive for HPV 39.

Conclusions
This study provides valuable baseline data for future assessment of the impact of current prophylactic vaccination programs that is protective against the two most common oncogenic types of HPV found in cervical cancer, HPV-16 and HPV-18, but not against other high-risk mucosal HPVs, 39 and 45, reported in this population.
Adult-onset leukoencephalopathy, brain calcifications and cysts: a case report
Authors: Wang Yaming , Cheng Gang , Dong Chao , Zhang Jianning , Meng Yuhong 
Published: June 2013

Abstract

Introduction
Leukoencephalopathy, brain calcifications and cysts, known as Labrune syndrome, is a rare syndrome. The etiology is unknown; in some cases it is difficult to differentiate from Coats plus syndrome and diagnosed as cerebroretinal microangiopathy with calcifications and cysts. We present the case of a patient with adult leukoencephalopathy, brain calcifications and cysts and discuss recently described entities in view of the relevant literature.

Case presentation
A previously healthy 19-year-old Chinese man presented with weakness of his right limbs that rapidly worsened over a short interval. Computed tomography and magnetic resonance imaging showed numerous low-density cysts, calcifications, and abnormal signal change of white matter. A visual field examination showed irregular visual field defects in both eyes. A neuro-ophthalmologic examination did not find evidence of Coats retinopathy. A larger excisional biopsy was carried out and a diagnosis of leukoencephalopathy, brain calcifications and cysts was confirmed.

Conclusions
We present an example of adult-onset leukoencephalopathy, brain calcifications and cysts and have expanded the clinical spectrum of features associated with this syndrome. Previous reports have not, to the best of our knowledge, previously reported visual field defects. Based on the latest findings, we believe that leukoencephalopathy, brain calcifications and cysts and Coats plus syndrome are genetically distinct entities.
Djeen (Database for Joomla!’s Extensible Engine): a research information management system for flexible multi-technology project administration
Authors: Stahl Olivier , Duvergey Hugo , Guille Arnaud , Blondin Fanny , Vecchio Alexandre Del , Finetti Pascal , Granjeaud Samuel , Vigy Oana , Bidaut Ghislain 
Published: June 2013

Abstract

Background
With the advance of post-genomic technologies, the need for tools to manage large scale data in biology becomes more pressing. This involves annotating and storing data securely, as well as granting permissions flexibly with several technologies (all array types, flow cytometry, proteomics) for collaborative work and data sharing. This task is not easily achieved with most systems available today.

Findings
We developed Djeen (Database for Joomla!’s Extensible Engine), a new Research Information Management System (RIMS) for collaborative projects. Djeen is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance.

Conclusion
Djeen allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Projects are managed within a hierarchy and user permissions are finely-grained for each project, user and group.
Djeen Component source code (version 1.5.1) and installation documentation are available under CeCILL license from http://sourceforge.net/projects/djeen/files and supplementary material.
5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni
Authors: Fneich Sara , Dheilly Nolwenn , Adema Coen , Rognon Anne , Reichelt Michael , Bulla Jan , Grunau Christoph , Cosseau Céline 
Published: June 2013

Abstract

Background

Biomphalaria glabrata is the mollusc intermediate host for Schistosoma mansoni, a digenean flatworm parasite that causes human intestinal schistosomiasis. An estimated 200 million people in 74 countries suffer from schistosomiasis, in terms of morbidity this is the most severe tropical disease after malaria. Epigenetic information informs on the status of gene activity that is heritable, for which changes are reversible and that is not based on the DNA sequence. Epigenetic mechanisms generate variability that provides a source for potentially heritable phenotypic variation and therefore could be involved in the adaptation to environmental constraint. Phenotypic variations are particularly important in host-parasite interactions in which both selective pressure and rate of evolution are high. In this context, epigenetic changes are expected to be major drivers of phenotypic plasticity and co-adaptation between host and parasite. Consequently, with characterization of the genomes of invertebrates that are parasite vectors or intermediate hosts, it is also essential to understand how the epigenetic machinery functions to better decipher the interplay between host and parasite.

Methods
The CpGo/e ratios were used as a proxy to investigate the occurrence of CpG methylation in B. glabrata coding regions. The presence of DNA methylation in B. glabrata was also confirmed by several experimental approaches: restriction enzymatic digestion with isoschizomers, bisulfite conversion based techniques and LC-MS/MS analysis.

Results
In this work, we report that DNA methylation, which is one of the carriers of epigenetic information, occurs in B. glabrata; approximately 2% of cytosine nucleotides are methylated. We describe the methylation machinery of B. glabrata. Methylation occurs predominantly at CpG sites, present at high ratios in coding regions of genes associated with housekeeping functions. We also demonstrate by bisulfite treatment that methylation occurs in multiple copies of Nimbus, a transposable element.

Conclusions
This study details DNA methylation for the first time, one of the carriers of epigenetic information in B. glabrata. The general characteristics of DNA methylation that we observed in the B. glabrata genome conform to what epigenetic studies have reported from other invertebrate species.
Seroprevalence of Toxoplasma gondii in horses and donkeys in Yunnan Province, Southwestern China
Authors: Miao Qiang , Wang Xi , She Li-Na , Fan Ya-Ting , Yuan Fei-Zhou , Yang Jian-Fa , Zhu Xing-Quan , Zou Feng-Cai 
Published: June 2013

AbstractBackgroundToxoplasma gondiiis an intracellular protozoan parasite that infects almost all warm-blooded animals, including humans, with a worldwide distribution. There have been limited reports about the seroprevalence ofT.gondiiinfection in equids around the world and little is known about the seroprevalence ofT.gondiiin equids in southwestern China, in particular in Yunnan Province. The objective of the present investigation was to estimate the seroprevalence ofT.gondiiinfection in equids in this area.MethodsA total of 399 serum samples (266 from horses and 133 from donkeys) were collected in 2012, and assayed forT.gondiiantibodies by Indirect Haemagglutination (IHA) test using a commercially available kit.ResultsA total of 108 (27.1%) equids, including 81 (30.5%) horses and 27 (20.3%) donkeys were positive forT.gondiiantibodies, and the seroprevalence ranged from 18.8% to 37.5% among different sampling areas. The seroprevalence was 27.4% and 26.8% for male and female equids, respectively, and the difference was not statistically significant (P > 0.05). The seroprevalence ranged from 21% to 32.9% among different age groups, and the difference was not statistically significant (P > 0.05).ConclusionsThe results of the present survey indicated the existence of highT.gondiiseroprevalence in Yunnan Province, southwestern China, which has significant public health concern. Therefore, it is imperative that improved integrated measures be carried out to prevent and controlT.gondiiinfection in equids in the studied region.
Deletion of integrin-linked kinase from neural crest cells in mice results in aortic aneurisms and embryonic lethality
Authors: Arnold Thomas D. , Zang Keling , Vallejo-Illarramendi Ainara 
Published: June 2013

Summary
Neural crest cells (NCCs) participate in the remodeling of the cardiac outflow tract and pharyngeal arch arteries during cardiovascular development. Integrin-linked kinase (ILK) is a serine/threonine kinase and a major regulator of integrin signaling. It links integrins to the actin cytoskeleton and recruits other adaptor molecules into a large complex to regulate actin dynamics and integrin function. Using the Cre-lox system, we deleted Ilk from NCCs of mice to investigate its role in NCC morphogenesis. The resulting mutants developed a severe aneurismal arterial trunk that resulted in embryonic lethality during late gestation. Ilk mutants showed normal cardiac NCC migration but reduced differentiation into smooth muscle within the aortic arch arteries and the outflow tract. Within the conotruncal cushions, Ilk-deficient NCCs exhibited disorganization of F-actin stress fibers and a significantly rounder morphology with shorter cellular projections. Additionally, absence of ILK resulted in reduced in vivo phosphorylation of Smad3 in NCCs, which correlated with reduced αSMA levels. Our findings resemble those seen in Pinch1 and β1 integrin conditional mutant mice, and therefore support that, in neural crest-derived cells, ILK and Pinch1 act as cytoplasmic effectors of β1 integrin in a pathway that protects against aneurysms. In addition, our conditional Ilk mutant mice might prove useful as a model to study aortic aneurysms caused by reduced Smad3 signaling, as occurs in the newly described aneurysms-osteoarthritis syndrome, for example.
Selenium Coprecipitated with Barite in Marine Sediments as a Possible Redox Indicator
Authors: Tokunaga Kohei , Yokoyama Yuka , Kawagucci Shinsuke , Sakaguchi Aya , Terada Yasuko , Takahashi Yoshio 
Published: June 2013

Abstract
Micro X-ray fluorescence mapping and X-ray absorption near-edge structure spectra were successfully measured for selenium (Se) in barite formed in marine sediments, which showed that Se(IV) was mainly found in the barite. The results showed that (i) Se in natural barite can be detected by µ-XRF-XAFS, (ii) the presence of Se(IV) suggested that the barite was precipitated under suboxic conditions, and (iii) the oxidation state of Se in barite can be used as a redox indicator of the depositional environment.
Discovery of Synthetic Methoxy-substituted 4-Phenylbutyric Acid Derivatives as Chemical Chaperones
Authors: Mimori Seisuke , Okuma Yasunobu , Kaneko Masayuki , Kawada Koichi , Nomura Yasuyuki , Murakami Yasuoki , Hamana Hiroshi 
Published: June 2013

Abstract
In this study, we evaluated the chemical chaperone activity of synthetic 4-phenylbutyric acid (4-PBA) derivatives. These derivatives have a methoxy group at the benzene ring and/or longer or shorter fatty acid portions. Several 4-PBA derivatives demonstrated higher antiaggregation activity than 4-PBA. Moreover, 4-(4-methoxyphenyl)butanoic acid (7b) showed protective effects against endoplasmic reticulum stress-induced neuronal cell death.
Synthetic Utility of Propylphosphonic Anhydride–DMSO Media: An Efficient One-pot Three-component Synthesis of 2-Arylquinolines
Authors: Narasimhamurthy Kereyagalahally H , Chandrappa Siddappa , Kumar Kothanahally S Sharath , Swaroop Toreshettahally R , Rangappa Kanchugarakoppal S 
Published: June 2013

Abstract
Propylphosphonic anhydride (T3P®)–DMSO-mediated one-pot three-component synthesis which provides 2-arylquinolines in a single step from benzyl alcohols, anilines, and ethyl vinyl ether by the modified Povarov reaction has been demonstrated. T3P®–DMSO is a mild and low-toxic peptide coupling agent and an easy to handle reagent for bulk reactions at room temperature.
Generation, life course and news media use in Sweden 1986–2011
Authors: Westlund Oscar , Weibull Lennart 
Published: June 2013

It has been posited that different generations are largely influenced by the characteristics of the media landscape they inherit and grow into in their formative years. However, we also know from empirical studies that individual media use changes over the life course. At present no
empirical study has analysed and compared the use of several news media among different generations in relation to both life cycle factors and media development over significant periods of time. Hence, this article explores the topic through its cross-generational comparison of transforming
news media usage. As a point of departure, the generation analyses use the widely recognized classification of the dutifuls (1926–1945), the baby boomers (1946–1964), generation X (1965–1976) and the dotnets (1977–1995). Five analytically distinct media system eras,
covering 1986 to 2011, are utilized for embedding the empiric analyses into distinct media system contexts. The findings evidence the generational hypothesis on formative socialization, especially with regards to the dutifuls and the baby boomers. Nevertheless, age and life cycle are also
identified as critically important factors. The findings show that the elderly persist with legacy news media, while younger generations predominantly orient towards news platforms that have emerged in the digital mediascape, even though this traditional classification seems to be too broad
for analysis of media development. Consequently, researchers should ideally acknowledge this double effect of age in future research on media usage, as well as work further on developing relevant classifications of generation relevant research for our understanding of transforming media use.
On a shape design problem for one spectral functional
Authors: Gasimov Yusif S. 
Published: June 2013

Abstract.
In the work we deal with the eigenvalue problem for the elliptic operator with variable domain. The object under investigation is a functional involving eigenvalues of this operator. A formula for the first variation of the functional with respect to the domain is derived. A necessary condition for the optimal shape is obtained. Evident formulas are given for
the eigenvalues in the optimal domain for some particular cases.
Lostology: Transmedia storytelling and expansion/compression strategies
Authors: Scolari Carlos A. 
Published: June 2013

Abstract
The objective of this article is to analyze Lost from the perspective of transmedia storytelling and to propose a taxonomy of transmedia expansion/compression strategies. In the first section, the article presents the basic components of transmedia storytelling from a theoretical point of view that combines narratology and semiotics. After describing the most important components of Lost's transmedia fictional universe in the second section, the article presents a general description and taxonomy of expansion/compression narrative strategies based on traditional rhetorical categories. The article also analyzes “compressed texts” – like recapitulations – and their role inside the expansive strategies.
Worker Education Level is a Factor in Self‐compliance with Dust‐preventive Methods among Small‐scale Agate Industrial Workers
Authors: Aggarwal Bhagwan D. 
Published: June 2013

Worker Education Level is a Factor in Self‐compliance with Dust‐preventive Methods among Small‐scale Agate Industrial Workers: Bhagwan D. AGGARWAL. Environmental Carcinogen Unit, National Institute of Occupational Health (Indian Council of Medical Research), India—ObjectivesHigh incidences of silicosis are continuing to be reported among the agate workers of small‐scale household agate processing units in the Khambhat region of Gujarat (India). The objective of this study was to investigate reasons behind the high prevalence of silicosis, and factors affecting the noncompliance with preventive methods among agate workers.MethodsThe study was conducted using a questionnaire‐based structured interview method among 82 agate workers in Khambhat to assess their awareness level about silicosis and preventive methods, existing morbidity, worker's attitude toward health, and the prevalence of actual use of preventive methods to avoid silica exposure.ResultsThe majority of the workers (55%) were aware of silicosis and the harmful effects of silica dust exposure (72%) and knew about simple preventive methods to avoid silica dust exposure (80%), but only a minority of the workers (22%) were actually using the simple and available dust‐preventive methods. Only 9% of the uneducated workers were using the preventive methods, while usage was higher among educated workers (28%), who had five or more years of schooling, and these workers had fewer health conditions or less morbidity. Gender and job duration had no effect on the usage of dust‐preventive methods.ConclusionsThe data suggest that noncompliance with use of dust‐preventive methods could be the reason behind the higher prevalence of silicosis and health morbidity in agate workers, and that years of schooling plays a significant role in the increased usage and self‐compliance with dust‐preventive methods among agate workers.