bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular classification of breast carcinomas with particular emphasis on “basal‐like” carcinoma: A critical review
Authors: Lavasani Mohammad Ali , Moinfar Farid 
Published: January 2012

AbstractDuring the last 11 years, 5 molecular subtypes of breast carcinoma (luminal A, luminal B, Her2‐positive, basal‐like, and normal breast‐like) have been characterized and intensively studied. As genomic research evolves, further subtypes of breast cancers into new “molecular entities” are expected to occur. For example, a new and rare breast cancer subtype, known as claudin‐low, has been recently found in human carcinomas and in breast cancer cell lines. There is no doubt that global gene expression analyses using high‐throughput biotechnologies have drastically improved our understanding of breast cancer as a heterogeneous disease. The main question is, however, whether new molecular techniques such as gene expression profiling (or signature) should be regarded as the gold standard for identifying breast cancer subtypes. A critical review of the literature clearly shows major problems with current molecular techniques and classification including poor definitions, lack of reproducibility, and lack of quality control. Therefore, the current molecular approaches cannot be incorporated into routine clinical practice and treatment decision making as they are immature or even can be misleading. This review particularly focuses on the “basal‐like” breast cancer subtype that represents one of the most popular breast cancer “entities”. It critically shows major problems and misconceptions with and about this subtype and challenges the common claim that it represents a “distinct entity”. It concludes that the term “basal‐like” is misleading and states that there is no evidence that expression of basal‐type cytokeratins in a given breast cancer, regardless of other established prognostic factors, does have any impact on clinical outcome. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Comparison of a new immobilized Fe3+ catalyst with homogeneous Fe3+–H2O2 system for degradation of 2,4‐dinitrophenol
Authors: Ghosh Prabir , Kumar Chandra , Samanta Amar Nath , Ray Subhabrata 
Published: January 2012

AbstractBACKGROUND: Heterogeneous Fenton catalysts have been used to treat various organic pollutants in an aqueous environment. The present study has investigated the degradation of 2,4‐dinitrophenol (2,4‐DNP), a priority pollutant generated by such industries as pharmaceuticals, pesticides, pigments and dyes. Degradation of 2,4‐DNP (100 mg L−1) was studied using Fe3+ loaded on Al2O3 as a heterogeneous catalyst in the presence of H2O2, and the efficiency compared with the homogeneous Fe3+/H2O2 based Fenton‐like process. The effect of different parameters for both processes, such as catalyst loading, H2O2 concentration, initial solution pH, initial substrate concentration and temperature were investigated and the optimum operating conditions determined.RESULTS: Under optimal operating conditions of the homogeneous system ([Fe3+] 125 mg L−1; [H2O2] 250 mg L−1; pH 3; room temperature), 92.5% degradation was achieved in 35 min for an initial 2,4‐DNP concentration of 100 mg L−1. In the case of immobilized Fe (Fe3+–Al2O3 catalyst), degradation improved to 98.7% under the condition 10 wt% [Fe3+–Al2O3] 1 g L−1 catalyst loading; [H2O2] 250 mg L−1; pH 3; at room temperature for the same duration.CONCLUSIONS: This study demonstrated the stability and reusability of the prepared heterogeneous catalyst. This process is a viable technique for treatment of aqueous solutions containing contaminants. Copyright © 2012 Society of Chemical Industry
Low turnover osteoporosis in sheep induced by hypothalamic‐pituitary disconnection
Authors: Beil Frank Timo , Oheim Ralf , Barvencik Florian , Hissnauer Tim N. , Pestka Jan M. , Ignatius Anita , Rueger Johannes M. , Schinke Thorsten , Clarke Iain J. , Amling Michael , Pogoda Pia 
Published: January 2012

AbstractThe hypothalamus is of critical importance in regulating bone remodeling. This is underscored by the fact that intracerebroventricular‐application of leptin in ewe leads to osteopenia. As a large animal model of osteoporosis, this approach has some limitations, such as high technical expenditure and running costs. Therefore we asked if a surgical ablation of the leptin signaling axis would have the same effects and would thereby be a more useful model. We analyzed the bone phenotype of ewe after surgical hypothalamo‐pituitary disconnection (HPD + OVX) as compared to control ewe (OVX) after 3 and 12 months. Analyses included histomorphometric characterization, micro‐CT and measurement of bone turnover parameters. Already 3 months after HPD we found osteopenic ewe with a significantly decreased bone formation (69%) and osteoclast activity (49%). After a period of 12 months the HPD group additionally developed an (preclinical) osteoporosis with significant reduction (33%) of femoral cortical thickness, as compared to controls (OVX). Taken together, HPD leads after 12 month to osteoporosis with a reduction in both trabecular and cortical bone caused by a low bone turnover situation, with reduced osteoblast and osteoclast activity, as compared to controls (OVX). The HPD‐sheep is a suitable large animal model of osteoporosis. Furthermore our results indicate that an intact hypothalamo‐pituitary axis is required for activation of bone turnover. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1254–1262, 2012
Improving fixation strength of pedicle screw by microarc oxidation treatment: An experimental study of osteoporotic spine in sheep
Authors: Shi Lei , Wang Ling , Zhang Yang , Guo Zheng , Wu Zi‐xiang , Liu Da , Gao Ming‐xuan , Chen Huan , Fu Suo‐chao , Lei Wei 
Published: January 2012

AbstractFailure of fixation caused by loosening of pedicle screws in osteoporosis is a problem in spinal surgery. We compared the in vivo fixation strength between pedicle screws treated with microarc oxidation (MAO) and untreated screws in an osteoporotic model of ovariectomized sheep. The MAO treated and untreated screws were placed in lumbar vertebral bodies. After 3 months of implantation, biomechanical tests, micro‐CT analysis, and histological observations were conducted to examine the performance of the two groups. At time 0, no significant difference was found between the two groups in biomechanical tests (p > 0.05); 3 months later, higher pull‐out strength and load with less displacement were detected in the MAO‐treated group (p < 0.05). Micro‐CT analysis showed that the tissue mineral density, bone volume fraction, trabecular thickness, and trabecular number in the MAO‐treated group were all higher than those in untreated group (p < 0.05), and trabecular spacing was smaller (p < 0.05). Histologically, the bone–implant interface in the MAO‐treated group was better than that in untreated group (p < 0.05). In conclusion, pedicle screws with a bioactive surface treated by MAO can improve screw fixation strength in osteoporotic spines in sheep. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1296–1303, 2012
Droplet size control with methanol‐repellent surface in a sampling device for continuous annular electrochromatography
Authors: Wang Qi , Rebrov Evgeny V. , Hessel Volker 
Published: January 2012

AbstractThe eluent droplet size defines the number of sampling compartments in a continuously operated annular electrochromatograph and therefore influences separation efficiency. In this work, an assembly of two capillaries, a feeding capillary on the top and a receiving capillary placed under it, has been investigated to control droplet size. The receiving capillary prevents the liquid droplet formation beyond a critical size, which reduces the volume of sampling compartment as compared with the case of the electrolyte flow driven solely by gravity. With a receiving capillary, the electrolyte droplet size was reduced from 1.5 to 0.46 mm. Further decrease of droplet size was not possible due to a so‐called droplet jump upwards effect which has been observed on a hydrophilic glass surface with water. A typical electrolyte used in CAEC has high methanol content. In an attempt to improve the methanol‐repellent properties of the glass surface, two approaches have been implemented: (i) self‐assembled chemisorbed monolayers of an alkylsiloxane and (ii) fabrication of a nano‐pin film. The methanol‐repellent surface of the feeding capillary suppressed the droplet jump upwards effect. The surface remained methanol repellent in different solutions with lower polarity than that of water.
On holomorphic polydifferentials in positive characteristic
Authors: Karanikolopoulos Sotiris 
Published: January 2012

AbstractLet F/E be an abelian Galois extension of function fields over an algebraic closed field K of characteristic p > 0. Denote by G the Galois group of the extension F/E. In this paper, we study Ω(m), the space of holomorphic m‐(poly)differentials of the function field of F when G is cyclic or a certain elementary abelian group of order pn; we give bases for each case when the base field is rational, introduce the Boseck invariants and give an elementary approach to the G module structure of Ω(m) in terms of Boseck invariants. The last computation is achieved without any restriction on the base field in the cyclic case, while in the elementary abelian case it is assumed that the base field is rational. Finally, an application to the computation of the tangent space of the deformation functor of curves with automorphisms is given.
A model structure approach to the finitistic dimension conjectures
Authors: Cortés Izurdiaga M. , Estrada S. , Guil Asensio P. A. 
Published: January 2012

AbstractWe explore the interlacing between model category structures attained to classes of modules of finite \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$\mathcal {X}$\end{document}‐dimension, for certain classes of modules \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$\mathcal {X}$\end{document}. As an application we give a model structure approach to the finitistic dimension conjectures and present a new conceptual framework in which these conjectures can be studied.
Inversion formula for the windowed Fourier transform
Authors: Sun W. 
Published: January 2012

AbstractIn this paper, we study the inversion formula for recovering a function from its windowed Fourier transform. We give a rigorous proof for an inversion formula which is known in engineering. We show that the integral involved in the formula is convergent almost everywhere on \documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$\mathbb {R}$\end{document} as well as in Lp for all 1 < p < ∞ if the function to be reconstructed is.
Intervention‐based multidimensional phase unwrapping using recursive orthogonal referring
Authors: Liu Junmin , Drangova Maria 
Published: January 2012

AbstractWe present a new intervention‐based phase unwrapping algorithm, which solves the inherent integration‐path‐dependent problem (typically resulting in streaks), by using a 2D recursive orthogonal referring (PUROR) approach. The streaks were removed by three consecutive procedures: intra‐image phase unwrapping, inter‐image cross‐referring a “good‐strip,” and cross‐referring line segments. The application of these procedures results in streak‐free 2D phase images. The phase inconsistencies across slices in a 3D image were removed using a hybrid 3D PUROR algorithm: the two step approach involves stacking the individual slices, by using the mean phase values of each slice, then applying the 2D PUROR algorithm to reformatted 2D images that include the slice direction. The described approach was tested with in vivo multislice phase images acquired in the axial, sagittal, and coronal orientation. The results of the unwrapped phase volume recovered using the PUROR algorithm have equivalent quality to that achieved by using established methods, but the PUROR algorithm is about two orders of magnitude faster (between 1 and 5 s per 256 × 256 slice; independent of slice orientation and echo time). Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Robust and adaptive multigrid methods: comparing structured and algebraic approaches
Authors: MacLachlan S.P. , Moulton J.D. , Chartier T.P. 
Published: January 2012

SUMMARYAlthough there have been significant advances in robust algebraic multigrid (AMG) methods in recent years, numerical studies and emerging hardware architectures continue to favor structured‐grid approaches. Specifically, implementations of logically structured robust variational multigrid algorithms, such as the black box multigrid (BoxMG) solver, have been shown to be 10 times faster than AMG for three‐dimensional heterogeneous diffusion problems on structured grids. BoxMG offers important features such as operator‐induced interpolation for robustness, while taking advantage of direct data access and bounded complexity in the Galerkin coarse‐grid operator. Moreover, because BoxMG uses a variational framework, it can be used to explore advances of modern adaptive AMG approaches in a structured setting. In this paper, we show how to extend the adaptive multigrid methodology to the BoxMG setting. This extension not only retains the favorable properties of the adaptive framework but also sheds light on the relationship between BoxMG and AMG. In particular, we show how classical BoxMG can be viewed as a special case of classical AMG and how this viewpoint leads to a richer family of adaptive BoxMG approaches. We present numerical results that explore this family of adaptive methods and compare its robustness and efficiency to the classical BoxMG solver.Copyright © 2012 John Wiley & Sons, Ltd.
A new tool for the assessment of satisfaction with iron chelation therapy (ICT‐Sat) for patients with β‐thalassemia major
Authors: Elalfy Mohsen S. , Massoud Walid , Elsherif Nayera H. , Labib Jonair H. , Elalfy Omar M. , Elaasar Safaa , von Mackensen Sylvia 
Published: January 2012

AbstractBackgroundHigh satisfaction with iron chelation is a major determinant for adherence to ICT in beta‐thalassaemia major (β‐TM) patients. In this study, a new tool to assess different domains of satisfaction for available forms of ICT was developed and validated. The impact of patients' satisfaction with ICT has been tested.MethodsItems were generated via focus groups and a preliminary version with 24 items (ICT‐Sat) with an additional item for treatment preference and a knowledge questionnaire (KQ) was developed. 170 β‐TM patients from three Thalassaemia centers in Egypt, aged 2–32 years received three questionnaires to fill in; the new ICT‐Sat, a KQ, and a previously validated tool for satisfaction with ICT (SICT) and retested 4–6 weeks later to ensure re‐test reliability. Type of chelation, drug related adverse events, compliance with ICT, and serum ferritin level (SF) during the year prior to the study as well as available cardiac T2*data were recorded.ResultsOne hundred and fifty two β‐TM patients completed all questionnaires; median age was 12 years. The final 15 remaining ICT‐Sat items, yielding to four domain scores, explained 70.6% of the total variance. The “perceived effectiveness” and “fear and worries” domains of the ICT‐Sat correlated significantly with the domains “perceived effectiveness” and “acceptance” of the SICT. Patients treated with oral ICT were more satisfied with perceived effectiveness, and their side effects.ConclusionsA new clinically based ICT‐Sat tool was developed and revealed good psychometric characteristics. Adherence to ICT was better correlated with “perceived effectiveness” and SF level. Pediatr Blood Cancer 2012; 58: 910–915. © 2012 Wiley Periodicals, Inc.
Massive conformation change in the prion protein: Using dual‐basin structure‐based models to find misfolding pathways
Authors: Singh Jesse P. , Whitford Paul C. , Hayre N. R. , Onuchic José , Cox Daniel L. 
Published: January 2012

AbstractWe employ all‐atom structure‐based models with a force field with multiple energetic basins for the C‐terminal (residues 166–226) of the mammalian prion protein. One basin represents the known alpha‐helical (αH) structure while the other represents the same residues in a left‐handed beta‐helical (LHBH) conformation. The LHBH structure has been proposed to help describe one class of in vitro grown fibrils, as well as possibly self‐templating the conversion of normal cellular prion protein to the infectious form. Yet, it is unclear how the protein may make this global rearrangement. Our results demonstrate that the conformation changes are not strongly limited by large‐scale geometry modification and that there may exist an overall preference for the LHBH conformation. Furthermore, our model presents novel intermediate trapping conformations with twisted LHBH structure. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Signatures of the ATP‐binding pocket as a basis for structural classification of the serine/threonine protein kinases of gram‐positive bacteria
Authors: Zakharevich Natalia V. , Osolodkin Dmitry I. , Artamonova Irena I. , Palyulin Vladimir A. , Zefirov Nikolay S. , Danilenko Valery N. 
Published: January 2012

AbstractEukaryotic‐like serine/threonine protein kinases (ESTPKs) are widely spread throughout the bacterial genomes. These enzymes can be potential targets of new antibacterial drugs useful for the treatment of socially important diseases such as tuberculosis. In this study, ESTPKs of pathogenic, probiotic, and antibiotic‐producing Gram‐positive bacteria were classified according to the physicochemical properties of amino acid residues in the ATP‐binding site of the enzyme. Nine residues were identified that line the surface of the adenine‐binding pocket, and ESTPKs were classified based on these signatures. Twenty groups were discovered, five of them containing >10 representatives. The two most abundant groups contained >150 protein kinases that belong to the various branches of the phylogenetic tree, whereas certain groups are genus‐ or even species‐specific. Homology modeling of the typical representatives of each group revealed that the classification is reliable, and the differences between the protein kinase ATP‐binding pockets predicted based on their signatures are apparent in their structure. The classification is expected to be useful for the selection of targets for new anti‐infective drugs. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
INFLUENCE OF ENVIRONMENTAL INSTABILITY OF GROUNDWATER‐FED STREAMS ON HYPORHEIC FAUNA, ON A GLACIAL FLOODPLAIN, DENALI NATIONAL PARK, ALASKA
Authors: Crossman J. , Bradley C. , Milner A. , Pinay G. 
Published: January 2012

ABSTRACTMacroinvertebrate community distributions were investigated within the benthic and hyporheic zone of five groundwater‐fed streams, on a floodplain terrace, in a glacierized catchment in Alaska, in summer 2008. The streams were characterized by a distinct gradient in environmental instability and provided an opportunity to determine whether the local variability in environmental instability of groundwater‐fed streams (reflecting differences in lengths of groundwater flow pathways) are of sufficient magnitude and frequency to influence macroinvertebrate community distribution. Individual measures of surface‐water temperature, streamflow, streambed stability and sediment size were incorporated into a multivariate index of environmental instability (IEI), using principal components analysis. In the hyporheic zone, a logarithmic association was observed between macroinvertebrate diversity and IEI and a quadratic association between abundance and IEI. The increase in diversity along the gradient of instability reflected a greater evenness of taxa caused by reduction in abundance of Chironomidae, combined with an increase in abundance of several less dominant taxa (Limnephilidae, Empididae, Baetidae and Simuliidae). At the surface, a quadratic association between diversity and IEI was observed, consistent with the intermediate disturbance hypothesis.Chironomidae, Nemouridae and Empididae presented contrasting surface and hyporheic distributions, indicating use of the hyporheic zone as a refuge. Moreover, covariance in the surface and hyporheic distribution of Limnephilidae and Chloroperlidae suggested the use of the hyporheic zone as an extension of the benthic habitat. The data indicate that local variability in environmental conditions between groundwater‐fed streams is sufficient to induce differences in macroinvertebrate communities and in the response of individual taxa. Copyright © 2012 John Wiley & Sons, Ltd.
Guiding explanation construction by children at the entry points of learning progressions
Authors: Songer Nancy Butler , Gotwals Amelia Wenk 
Published: January 2012

AbstractPolicy documents in science education suggest that even at the earliest years of formal schooling, students are capable of constructing scientific explanations about focal content. Nonetheless, few research studies provide insights into how to effectively provide scaffolds appropriate for late elementary‐age students' fruitful creation of scientific explanations. This article describes two research studies to address the question, what makes explanation construction difficult for elementary students? The studies were conducted in urban fourth, fifth, and sixth grade classrooms where students were learning science through curricular units that contained 8 weeks of scaffold‐rich activities focused on explanation construction. The first study focused on the kind and amount of information scaffold‐rich assessments provided about young students' abilities to construct explanations under a range of scaffold conditions. Results demonstrated that fifth and sixth grade tests provided strong information about a range of students' abilities to construct explanations under a range of supported conditions. On balance, the fourth grade test did not provide as much information, nor was this test curricular‐sensitive. The second study provided information on pre–post test achievement relative to the amount of curricular intervention utilized over the 8‐week time period with each cohort. Results demonstrated that when taking the amount of the intervention into account, there were strong learning gains in all three grade‐level cohorts. In conjunction with the pre–post study, a type‐of‐error analysis was conducted to better understand the nature of errors among younger students. This analysis revealed that our youngest students generated the most incomplete responses and struggled in particular ways with generating valid evidence. Conclusions emphasize the synergistic value of research studies on scaffold‐rich assessments, curricular scaffolds, and teacher guidance toward a more complete understanding of how to support young students' explanation construction. © 2011 Wiley Periodicals, Inc. J Res Sci Teach 49: 141–165, 2012