bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous Dual-Color Fluorescence Microscope: A Characterization Study
Authors: Li Zheng , Chen Xiaodong , Ren Liqiang , Song Jie , Li Yuhua , Zheng Bin , Liu Hong 
Published: January 2015

Background: High spatial resolution and geometric accuracy is crucial for chromosomal analysis of clinical cytogenetic applications. High resolution and rapid simultaneous acquisition of multiple fluorescent wavelengths can be achieved by utilizing concurrent imaging with multiple detectors. However, such class of microscopic systems functions differently from traditional fluorescence microscopes.Objective: To develop a practical characterization framework to assess and optimize the performance of a high resolution and dual-color fluorescence microscope designed for clinical chromosomal analysis.Methods: A dual-band microscopic imaging system utilizes a dichroic mirror, two sets of specially selected optical filters, and two detectors to simultaneously acquire two fluorescent wavelengths. The system’s geometric distortion, linearity, the modulation transfer function, and the dual detectors’ alignment were characterized.Results: Experiment results show that the geometric distortion at lens periphery is less than 1%. Both fluorescent channels show linear signal responses, but there exists discrepancy between the two due to the detectors’ non-uniform response ratio to different wavelengths. In terms of the spatial resolution, the two contrast transfer function curves trend agreeably with the spatial frequency. The alignment measurement allows quantitatively assessing the cameras' alignment. A result image of adjusted alignment is demonstrated to show the reduced discrepancy by using the alignment measurement method.Conclusions: In this paper, we present a system characterization study and its methods for a specially designed imaging system for clinical cytogenetic applications. The presented characterization methods are not only unique to this dual-color imaging system but also applicable to evaluation and optimization of other similar multi-color microscopic image systems for improving their clinical utilities for future cytogenetic applications.
Cartilage Oligomeric Matrix Protein (COMP)-Mediated Cell Differentiation to Proteolysis Mechanism Networks from Human Normal Adjacent Tissues to Lung Adenocarcinoma
Authors: Wang Lin , Huang Juxiang , Jiang Minghu , Diao Haizhen , Zhou Huilei , Li Xiaohe , Chen Qingchun , Jiang Zhenfu , Feng Haitao , Wolfl Stefan 
Published: January 2015

Background: To understand cartilage oligomeric matrix protein (COMP) mechanism network from human normal adjacent tissues to lung adenocarcinoma.Methods:COMPcomplete different activated (all no positive correlation, Pearson CC< 0.25) and uncomplete (partly no positive correlation exceptCOMP, Pearson CC< 0.25) network were identified in higher lung adenocarcinoma compared with lower human normal adjacent tissues from the correspondingCOMP-stimulated (≥0.25) or inhibited (Pearson CC≤−0.25) overlapping molecules of Pearson correlation coefficient (CC) and GRNInfer, respectively.COMPcomplete different activated and inhibited (all no positive correlation, Pearson CC< 0.25) mechanisms networks of higher lung adenocarcinoma and lower human normal adjacent tissues were constructed by integration of Pearson CC, GRNInfer and GO. As visualized by integration of GO, KEGG, GenMAPP, BioCarta and Disease, we deduced COMP complete different activated and inhibited network in higher lung adenocarcinoma and lower human normal adjacent tissues.Results: As visualized by GO, KEGG, GenMAPP, BioCarta and disease database integration, we proposed mainly that the mechanism and function ofCOMPcomplete different activated network in higher lung adenocarcinoma was involved inCOMPactivation with matrix-localized insulin-like factor coupling carboxypeptidase to metallopeptidase-induced proteolysis, whereas the corresponding inhibited network in lower human normal adjacent tissues participated inCOMPinhibition with nucleus-localized vasculogenesis, B and T cell differentiation and neural endocrine factors coupling pyrophosphatase-mediated proteolysis. However,COMPcomplete different inhibited network in higher lung adenocarcinoma includedCOMPinhibition with nucleus-localized chromatin maintenance, licensing and assembly factors coupling phosphatase-inhibitor to cytokinesis regulators-mediated cell differentiation, whereas the corresponding activated network in lower human normal adjacent tissues containedCOMPactivation with cytolplasm-localized translation elongation factor coupling fucosyltransferase to ubiquitinprotein ligase-induced cell differentiation.Conclusion:COMPdifferent networks were verified not only by complete and uncompleteCOMPactivated or inhibited networks within human normal adjacent tissues or lung adenocarcinoma, but also byCOMPactivated and inhibited network between human normal adjacent tissues and lung adenocarcinoma.
Expression of WW Domain-Containing Oxidoreductase WOX1 in Human Nervous System Tumors
Authors: Chiang Ming-Fu , Chen Shur-Tzu , Lo Chen-Peng , Sze Chun-I , Chang Nan-Shan , Chen Yu-Jen 
Published: January 2015

Background and ObjectiveS: We aimed to evaluate the expression levels of the tumor suppressor WOX1 in nervous system tumors and its co-expression with p53 and neurofibromatosis type 2/merlin (NF2) tumor suppressor gene products.Methods: Immunohistochemistry, western blotting andin situhybridization were used for WOX1 protein and WWOX mRNA expression. Immunofluorescence and electron microscopical immunohistochemistry were performed for colocalization of gene products.Results: WOX1 expression is low in normal cortical neurons, mainly on the axon fibers, whereas there is moderate to high immunoreactivity in the cytosol and nuclei of certain tumor cells. In the microcystic (WHO grade I) and malignant (WHO grade III) meningiomas, WOX1 expression is intense, but various in transitional (WHO grade I) and atypical (WHO grade II) subtypes. WOX1 levels are moderate to high in the menigiotheliomatous area, but relatively low in the fibroblastic area. WOX1 and NF2/merlin, but not p53, colocalized in certain tumor cells, primarily at the borders of nuclei. Schwannoma and astrocytoma specimens stained moderately to strongly positive for the WOX1 protein. Interestingly, the expression of WOX1, NF2/merlin and mutant p53 is intense in high grade glioblastoma, but WOX1 expression is low in metastatic carcinoma or adenocarcinoma.Conclusions: The expression of WOX1 on different types of nervous system tumors, including primary and metastatic tumors, is differential.
Turning Telomerase into a Jekyll and Hyde Case?
Authors: Wellinger Raymund J. 
Published: January 2015

Abstract
Summary: It may be possible to coerce telomerase to incorporate modified guanine nucleotides into telomeric repeat DNA, thereby seriously compromising the functionality of the telomeres. Thus, a guanine analogue such as 6-thio-dG could turn active telomerase into a chromosome de-protecting enzyme, the opposite of what it is normally, namely a chromosome-protecting enzyme. Cancer Discov; 5(1); 19–21. ©2015 AACR.
See related article by Mender et al., p. 82
Czym jest i co zawiera „Słownik mówionej polszczyzny pónocnokresowej”
Authors: Grek-Pabisowa Iryda , Biesiadowska-Magdziarz Beata , Jankowiak Mirosław , Ostrówka Małgorzata 
Published: January 2015

What is ”A Dictionary of oral Polish language of the north-eastern borderland” and what does it include?A regional variety of the Polish language of the north-eastern borderland in both oral and written forms has been functioning in Belarus, Lithuania and Latvia (former Polish Livonia) for several centuries. In 2000, The Team for Research on the Polish Language of the North-Eastern Borderland of the Institute of Slavic Studies of PAS came up with an idea of creating A Dictionary of oral Polish language of the north-eastern borderland. First, publications containing patterns of the Polish language, credibly recorded, were collected. There were more and more new studies, and the material was enriched with many new lexemes as well as their new variants or better exemplifications. Therefore, the lexical collection continued and was completed in 2012. At the same time the team researchers carried out excerpting from earlier texts, choosing examples, searching for parallel forms of lexemes, blending the material in dictionary units, i.e. establishing the form of a dictionary entry. In this way the corpus of the dictionary was written, following a formula created by the team.The article presents methodology of creating the Dictionary, its material basis, short description of lexical items included and the content of an entry. Czym jest i co zawiera „Słownik mówionej polszczyzny pónocnokresowej”Regionalna odmiana polszczyzny północnokresowej w postaci języka mówionego i pisanego funkcjonowała na obszarze Białorusi, Litwy i Łotwy (dawne Inflanty Polskie) od kilku wieków.W roku 2000 w Zespole Badań Polszczyzny Północnokresowej IS PAN powstał pomysł opracowania Słownika mówionej polszczyzny północnokresowej. Przez pierwsze lata wyszukiwano i gromadzono publikacje zawierające zarejestrowane w sposób wiarygodny wzorce mowy polskiej na interesującym nas terenie. Nowych opracowań stale przybywało, materiał powiększał się o nowe leksemy lub ich nowe postaci czy lepszą egzemplifikację. Dlatego też uzupełnianie zbioru leksykalnego zamknięto datą publikacji wydanych w roku 2012. Równolegle z uzupełnieniami pochodzącymi z nowo pojawiających się prac prowadzono ekscerpcję z tekstów wcześniejszych, dobór przykładów, wyszukiwanie paralelnych postaci leksemów i scalanie materiałów w jednostki słownikowe, czyli ustalanie postaci hasła. W ten sposób powstał korpus Słownika, który opracowywano według ułożonej przez zespół formuły. Artykuł przedstawia metodologię tworzenia Słownika, jego podstawę materiałową, krótką charakterystykę leksyki, którą zawiera oraz zawartość artykułu hasłowego.
S3T Stability of the Homogeneous State of Barotropic Beta-Plane Turbulence
Authors: Bakas Nikolaos A. , Constantinou Navid C. , Ioannou Petros J. 
Published: January 2015

Abstract
Zonal jets and nonzonal large-scale flows are often present in forced–dissipative barotropic turbulence on a beta plane. The dynamics underlying the formation of both zonal and nonzonal coherent structures is investigated in this work within the statistical framework of stochastic structural stability theory (S3T). Previous S3T studies have shown that the homogeneous turbulent state undergoes a bifurcation at a critical parameter and becomes inhomogeneous with the emergence of zonal and/or large-scale nonzonal flows and that these statistical predictions of S3T are reflected in direct numerical simulations. In this paper, the dynamics underlying the S3T statistical instability of the homogeneous state as a function of parameters is studied. It is shown that, for weak planetary vorticity gradient β, both zonal jets and nonzonal large-scale structures form from upgradient momentum fluxes due to shearing of the eddies by the emerging infinitesimal flow. For large β, the dynamics of the S3T instability differs for zonal and nonzonal flows but in both the destabilizing vorticity fluxes decrease with increasing β. Shearing of the eddies by the mean flow continues to be the mechanism for the emergence of zonal jets while nonzonal large-scale flows emerge from resonant and near-resonant triad interactions between the large-scale flow and the stochastically forced eddies. The relation between the formation of large-scale structure through modulational instability and the S3T instability of the homogeneous state is also investigated and it is shown that the modulational instability results are subsumed by the S3T results.
Impact of Anomalous Northward Oceanic Heat Transport on Global Climate in a Slab Ocean Setting
Authors: L’Hévéder Blandine , Codron Francis , Ghil Michael 
Published: January 2015

Abstract
This paper explores the impact of anomalous northward oceanic heat transport on global climate in a slab ocean setting. To that end, the GCM LMDZ5A of the Laboratoire de Météorologie Dynamique is coupled to a slab ocean, with realistic zonal asymmetries and seasonal cycle. Two simulations with different anomalous surface heating are imposed: 1) uniform heating over the North Atlantic basin and 2) concentrated heating in the Gulf Stream region, with a compensating uniform cooling in the Southern Ocean in both cases. The magnitudes of the heating and of the implied northward interhemispheric heat transport are within the range of current natural variability. Both simulations show global effects that are particularly strong in the tropics, with a northward shift of the intertropical convergence zone (ITCZ) toward the heating anomalies. This shift is accompanied by a northward shift of the storm tracks in both hemispheres. From the comparison between the two simulations with different anomalous surface heating in the North Atlantic, it emerges that the global climate response is nearly insensitive to the spatial distribution of the heating. The cloud response acts as a large positive feedback on the oceanic forcing, mainly because of the low-cloud-induced shortwave anomalies in the extratropics. While previous literature has speculated that the extratropical Q flux may impact the tropics by the way of the transient eddy fluxes, it is explicitly demonstrated here. In the midlatitudes, the authors find a systematic northward shift of the jets, as well as of the associated Ferrel cells, storm tracks, and precipitation bands.
Quadrature-Free Implementation of a Discontinuous Galerkin Global Shallow-Water Model via Flux Correction Procedure
Authors: Nair Ramachandran D. 
Published: January 2015

Abstract
The discontinuous Galerkin (DG) discretization relies on an integral (weak) formulation of the hyperbolic conservation law, which leads to the evaluation of several surface and line integrals for multidimensional problems. An alternative formulation of the DG method is possible under the flux reconstruction (FR) framework, where the equations are solved in differential form and the discretization is free from quadrature rules, resulting in computationally efficient algorithms. The author has implemented a quadrature-free form of the nodal DG method based on the FR approach combined with spectral differencing (SD), in a shallow-water (SW) model employing cubed-sphere geometry. The performance of the SD model is compared with the regular nodal DG variant of the SW model using several benchmark tests, including a viscous test case. A positivity-preserving local filter is tested for SD advection that removes spurious oscillations while being conservative and accurate. In this implementation, the SD formulation is found to be 18% faster than the DG method for inviscid SW tests cases and 24% faster for the viscous case. The results obtained by the SD formulation are on par with the regular nodal DG formulation in terms of accuracy and convergence.
Cultural Determinants of Optimal Breastfeeding Practices among Indigenous Mam-Mayan Women in the Western Highlands of Guatemala
Authors: Wren Hilary M. , Solomons Noel W. , Chomat Anne Marie , Scott Marilyn E. , Koski Kristine G. 
Published: January 2015

Background: Among indigenous Mam-Mayan women, breastfeeding practices may be intertwined with cultural influences during the early postpartum period. Objectives: Our study explored whether beliefs regarding transmission of emotions through breast milk, the feeding of agüitas or temascal (traditional sauna) use were associated with achievement of the World Health Organization infant feeding recommendations and if these cultural practices served as moderators of the relationship between optimal breastfeeding practices and infant anthropometry. Methods: We recruited 190 mother-infant dyads at infant age < 46 days. Data on breastfeeding and cultural practices were collected via questionnaire. Infant length, weight, and head circumference were measured and z scores were calculated. Multiple linear and logistic regression analyses were used to examine determinants of initiation of breastfeeding within 1 hour, breastfeeding frequency, breastfeeding exclusivity, and infant weight-for-age z score (WAZ). Results: Mothers who delivered at the traditional midwife’s house (odds ratio [OR] = 2.5) and those who did not believe in the transmission of susto (fright) through breast milk (OR = 2.4) were more likely to initiate breastfeeding within 1 hour postpartum. Higher breastfeeding frequency was observed among mothers who spent more time in the temascal. Initiating early breastfeeding within 1 hour postpartum was the sole infant feeding practice positively associated with exclusive breastfeeding and WAZ. Conclusions: Our investigation in the Western Highlands of Guatemala has highlighted the link between cultural practices and beliefs during lactation, breastfeeding practices and infant growth. Public health practitioners need to understand how local cultural practices influence early initiation of breastfeeding to promote adequate infant weight.
De novo assembly of bacterial transcriptomes from RNA-seq data
Authors: Tjaden Brian 
Published: January 2015

AbstractTranscriptome assays are increasingly being performed by high-throughput RNA sequencing (RNA-seq). For organisms whose genomes have not been sequenced and annotated, transcriptomes must be assembled de novo from the RNA-seq data. Here, we present novel algorithms, specific to bacterial gene structures and transcriptomes, for analysis of bacterial RNA-seq data and de novo transcriptome assembly. The algorithms are implemented in an open source software system called Rockhopper 2. We find that Rockhopper 2 outperforms other de novo transcriptome assemblers and offers accurate and efficient analysis of bacterial RNA-seq data. Rockhopper 2 is available at http://cs.wellesley.edu/~btjaden/Rockhopper.
Onion (Allium cepa L.) peel extract has anti-platelet effects in rat platelets
Authors: Ro Ju-Ye , Ryu Jin-Hyeob , Park Hwa-Jin , Cho Hyun-Jeong 
Published: January 2015

AbstractThe effects of onion peel extract (OPE) in collagen (5 μg/mL)-stimulated washed rat platelet aggregation were investigated. OPE inhibited platelet aggregationviainhibition of aggregation-inducing molecules, intracellular Ca2+and thromboxane A2(TXA2) by blocking cyclooxygenase-1 (COX-1) and TXA2synthase (TXAS) activities in a dose-dependent manner. In addition, OPE elevated the formation of cyclic adenosine monophosphate (cAMP), aggregation-inhibiting molecule, but not cyclic guanosine monophosphate (cGMP). High performance liquid chromatography (HPLC) analysis of OPE revealed that OPE contains quercetin, one of the major flavonoids, which has anti-platelet effect. In conclusion, we suggest that OPE is an effective inhibitor of collagen-stimulated platelet aggregationin vitro. Therefore, it can be a promising and safe strategy for anti-cardiovascular diseases.
Physico-chemical characterization and pharmacological evaluation of sulfated polysaccharides from three species of Mediterranean brown algae of the genus Cystoseira
Authors: Hadj Ammar Hiba , Lajili Sirine , Ben Said Rafik , Le Cerf Didier , Bouraoui Abderrahman , Majdoub Hatem 
Published: January 2015

Abstract

Background
Seaweed polysaccharides are highly active natural substances having valuable applications. The present study was conducted to characterize the physico-chemical properties of sulphated polysaccharides from three Mediterranean brown seaweeds (Cystoseira sedoides, Cystoseira compressa and Cystoseira crinita) and to evaluate their anti-radical, anti-inflammatory and gastroprotective activities.

Methods
The different rates of neutral sugars, uronic acids, L-fucose and sulphate content were determined by colorimetric techniques. The different macromolecular characteristics of isolated fucoidans were identified by size exclusion chromatography equipped with a triple detection: multiangle light scattering, viscometer and differential refractive index detectors, (SEC/MALS/VD/DRI). Anti-inflammatory activity was evaluated, using the carrageenan-induced rat paw edema test in comparison to the references drugs Acetylsalicylate of Lysine and Diclofenac. The gastroprotective activity was determined using HCl/EtOH induced gastric ulcers in rats and to examine the antioxidant effect of fucoidans in the three species, the free radical scavenging activity was determined using 1,1-diphenyl-2-picrylhydrazyl.

Results
The pharmacological evaluation of the isolated fucoidans for their anti-inflammatory, and their gastroprotective effect established that these products from C. sedoides, C. compressa and C. crinita exhibited a significant anti-inflammatory activity at a dose of 50 mg/kg, i.p; the percentages of inhibition of the oedema were 51%, 57% and 58% respectively. And, at the same dose, these fucoidans from C. sedoides and C. compressa showed a significant decrease of the intensity of gastric mucosal damages compared to a control group by 68%, whereas, the fucoidan from C. crinita produced a less gastroprotective effect. Furthermore, the isolated fucoidans exhibited a radical scavenging activity.

Conclusion
The comparative study of fucoidans isolated from three species of the genus Cystoseira showed that they have similar chemicals properties and relatives anti-radical, anti-inflammatory and gastroprotective activities which are found to be promising.
The capacity-building and science-enabling activities of the IUGONET for the solar-terrestrial research community
Authors: Yatagai Akiyo , Sato Yuka , Shinbori Atsuki , Abe Shuji , UeNo Satoru ,   IUGONET project team
Published: January 2015

Abstract

Background
This paper presents an overview of the capacity-building activities and science-enabling services of the Inter-university Upper atmosphere Global Observation NETwork (IUGONET) project. This Japanese program, which started in 2009, is building a metadata database (MDDB) of ground-based observations and is developing an analysis software to handle the data linked to the MDDB system for use by the solar-terrestrial physics community. Because the institutional members of the IUGONET are mainly universities in Japan, we explore tools that can contribute to advanced education as well as promote research activities.

Findings
In this paper, we describe the utilities of the IUGONET for education, including our capacity-building activities in developing countries. We have regularly facilitated training seminars for Japanese students on the use of our tools (IUGONET MDDB and the software), and we have held capacity-building seminars for young scientists in developing countries. In addition to the MDDB, we have prepared various ‘gateway’ tools for users who are unfamiliar with ‘keywords’ to search for data. One of these is a geographical display tool that uses Google Earth (KML file), which is included as supplemental material to this paper. The usefulness of the IUGONET has been proven over its first 5 years of operation by the increasing number of its users, which has led to the production of approximately 500 scientific papers, including 42 thesis papers.

Conclusions
The IUGONET community collaborates with the Scientific Committee on Solar-Terrestrial Physics program, not only in its scientific activities, but also in the establishment of E-infrastructure and capacity building.