bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heparanase-mediated cleavage of macromolecular heparin accelerates release of granular components of mast cells from extracellular matrices
Authors: Higashi Nobuaki , Waki Michihiko , Sue Mayumi , Kogane Yusuke , Shida Hiroaki , Tsunekawa Naoki , Hasan Ahasanul , Sato Takeshi , Kitahara Ayumi , Kasaoka Tatsuhiko , Hayakawa Yoshihiro , Nakajima Motowo , Irimura Tatsuro 
Published: December 2013

Heparanase cleaves macromolecular heparin in the secretory granules of connective tissue-type mast cells. We investigated roles of the cleavage under a microenvironment mimicking where the mast cells physiologically reside. A connective tissue-type mast cell line MST and mouse peritoneal cell-derived mast cells stored macromolecular heparin in the secretory granules. The cells expressing heparanase stored fragmented heparin (~10 kDa) due to heparanase-dependent cleavage of the heparin. We produced an artificial collagen-based extracellular matrix and placed the live cells or glycosaminoglycans purified from the cells in the matrix to measure the release of sulfated macromolecules into the medium. The sulfate-radiolabelled molecules from the degranulating heparanase-expressing cells and the purified glycosaminoglycans showed significantly greater release into the medium than those derived from mock cells, which was not the case in suspension culture. The mast cell granular enzyme chymase, but not β-hexosaminidase, showed significantly greater release from the degranulating heparanase-expressing cells than from mock cells. Purified chymase mixed with fragmented heparin derived from heparanase-expressing cells showed greater release from collagen gels than the enzyme alone or mixed with macromolecular heparin derived from mock cells. We propose that the cleavage of macromolecular heparin by heparanase accelerates the release of heparin and chymase from extracellular matrices.
Caveolin 1 is critical for abdominal aortic aneurysm formation induced by angiotensin II and inhibition of lysyl oxidase
Authors: Takayanagi Takehiko , Crawford Kevin J. , Kobayashi Tomonori , Obama Takashi , Tsuji Toshiyuki , Elliott Katherine J. , Hashimoto Tomoki , Rizzo Victor , Eguchi Satoru 
Published: December 2013

Although AngII (angiotensin II) and its receptor AT1R (AngII type 1 receptor) have been implicated in AAA (abdominal aortic aneurysm) formation, the proximal signalling events primarily responsible for AAA formation remain uncertain. Caveolae are cholesterol-rich membrane microdomains that serve as a signalling platform to facilitate the temporal and spatial localization of signal transduction events, including those stimulated by AngII. Cav1 (caveolin 1)-enriched caveolae in vascular smooth muscle cells mediate ADAM17 (a disintegrin and metalloproteinase 17)-dependent EGFR (epidermal growth factor receptor) transactivation, which is linked to vascular remodelling induced by AngII. In the present study, we have tested our hypothesis that Cav1 plays a critical role for the development of AAA at least in part via its specific alteration of AngII signalling within caveolae. Cav1−/− mice and the control wild-type mice were co-infused with AngII and β-aminopropionitrile to induce AAA. We found that Cav1−/− mice with the co-infusion did not develop AAA compared with control mice in spite of hypertension. We found an increased expression of ADAM17 and enhanced phosphorylation of EGFR in AAA. These events were markedly attenuated in Cav1−/− aortas with the co-infusion. Furthermore, aortas from Cav1−/− mice with the co-infusion showed less endoplasmic reticulum stress, oxidative stress and inflammatory responses compared with aortas from control mice. Cav1 silencing in cultured vascular smooth muscle cells prevented AngII-induced ADAM17 induction and activation. In conclusion, Cav1 appears to play a critical role in the formation of AAA and associated endoplasmic reticulum/oxidative stress, presumably through the regulation of caveolae compartmentalized signals induced by AngII.
Triple band‐notched UWB antenna based on SIR‐DGS and fork‐shaped stubs
Authors: Zhang Chaozhu , Zhang Jing , Li Lin 
Published: December 2013

A compact CPW‐fed triple band‐notched antenna for ultra‐wide bandwidth (UWB) application is presented. By introducing an stepped impedance resonator‐defected ground structure (SIR‐DGS) and fork‐shaped stubs, three sharp notches are achieved at frequencies of 3.5, 5.68 and 7.48 GHz. The proposed antenna working from 2.8 to 11.3 GHz with a voltage standing wave ratio of <2 is demonstrated, except for the selected notched bands. The main advantage of the antenna is that the frequency of the notched band can be tuned easily in a wide frequency range. A good agreement between the measurement and the simulation was achieved. The measurements confirm that the technique introduces negligible antenna radiation pattern distortion, except at the triple‐notched frequencies.
Edible oil structures at low and intermediate concentrations. I. Modeling, computer simulation, and predictions for X ray scattering
Authors: Pink David A. , Quinn Bonnie , Peyronel Fernanda , Marangoni Alejandro G. 
Published: December 2013

Triacylglycerols (TAGs) are biologically important molecules which form the recently discovered highly anisotropic crystalline nanoplatelets (CNPs) and, ultimately, the large-scale fat crystal networks in edible oils. Identifying the hierarchies of these networks and how they spontaneously self-assemble is important to understanding their functionality and oil binding capacity. We have modelled CNPs and studied how they aggregate under the assumption that all CNPs are present before aggregation begins and that their solubility in the liquid oil is very low. We represented CNPs as rigid planar arrays of spheres with diameter ≈50 nm and defined the interaction between spheres in terms of a Hamaker coefficient, A, and a binding energy, VB. We studied three cases: weak binding, |VB|/kBT ≪ 1, physically realistic binding, VB = Vd(R, Δ), so that |VB|/kBT ≈ 1, and Strong binding with |VB|/kBT ≫ 1. We divided the concentration of CNPs, ϕ, with 0≤ϕ= 10−2 (solid fat content) ≤1, into two regions: Low and intermediate concentrations with 0&lt;ϕ&lt;0.25 and high concentrations with 0.25 &lt; ϕ and considered only the first case. We employed Monte Carlo computer simulation to model CNP aggregation and analyzed them using static structure functions, S(q). We found that strong binding cases formed aggregates with fractal dimension, D, 1.7≤D≤1.8, in accord with diffusion limited cluster-cluster aggregation (DLCA) and weak binding formed aggregates with D=3, indicating a random distribution of CNPs. We found that models with physically realistic intermediate binding energies formed linear multilayer stacks of CNPs (TAGwoods) with fractal dimension D=1 for ϕ=0.06,0.13, and 0.22. TAGwood lengths were greater at lower ϕ than at higher ϕ, where some of the aggregates appeared as thick CNPs. We increased the spatial scale and modelled the TAGwoods as rigid linear arrays of spheres of diameter ≈500 nm, interacting via the attractive van der Waals interaction. We found that TAGwoods aggregated via DLCA into clusters with fractal dimension D=1.7−1.8. As the simulations were run further, TAGwoods relaxed their positions in order to maximize the attractive interaction making the process look like reaction limited cluster-cluster aggregation with the fractal dimension increasing to D=2.0−2.1. For higher concentrations of CNPs, many TAGwood clusters were formed and, because of their weak interactions, were distributed randomly with D=3.0. We summarize the hierarchy of structures and make predictions for X-ray scattering.
Celastrol increases glucocerebrosidase activity in Gaucher disease by modulating molecular chaperones
Authors: Yang Chunzhang , Swallows Cody L. , Zhang Chao , Lu Jie , Xiao Hongbin , Brady Roscoe O. , Zhuang Zhengping 
Published: December 2013

Significance
Gaucher disease (GD) is one of the most prevalent inherited metabolic storage disorders of humans. GD results from mutations in the gene coding for glucocerebrosidase (GCase) that often lead to protein misfolding and premature degradation. This study demonstrates that the small molecule celastrol prevents mutant GCase degradation by targeting the assembly of a heat-shock protein chaperone complex. Additionally, celastrol reorganizes the expression pattern of chaperone genes. Specifically, celastrol up-regulates genes coding for Heat-shock protein 70 (Hsp70), DnaJ homolog subfamily B members 1 and 9 (DNAJB1/9), and BAG family chaperone regulator 3 (BAG3). Celastrol stabilizes mutant GCase by specifically targeting BAG3. These findings provide insight into the molecular mechanisms underlying human disorders that result from abnormalities of protein stability.
Constructing the Self
Authors: Hardcastle Valerie Gray 
Published: December 2013

Constructing the Self analyzes the narrative conception of self, filling a serious gap in philosophy and grounding discussion in other disciplines. It answers the questions:
What are the connections between our interpretations, selfhood, and conscious phenomenal experience?Why do we believe that our interpretations of our life-defining events are narrative in nature?From the myriad of thoughts, actions, and emotions which constitute our experiences, how do we choose what is interpretively important, the tiny subset that composes the self?
By synthesizing the different approaches to understanding the self from philosophy of mind, developmental psychology, psychopathology, and cognitive science, this monograph gives us deeper insight into what being minded, being a person, and having a self are, as well as clarifies the difference and relation between conscious and unconscious mental states and normal and abnormal minds. The explication also affords new perspectives on human development and human emotion. (Series A)
The Rhetoric of Philosophy
Authors: Frogel Shai 
Published: December 2013

The book claims that philosophy can be defined by its distinct rhetoric. This rhetoric is shaped by two values: humanism and critique. Humanism is defined as preferring the individual human deliberation to any external authority or method. Self-conviction is the touchstone of truth in philosophy. Critique is defined as suspecting your beliefs and convictions. This is the reason why the book uses Nietzsche’s definition of "the will to truth" – "the will not to deceive, not even myself" – for explaining the nature of philosophical thinking and argumentation. This rhetorical analysis reveals that the danger of self-deception is a constitutive yet irresolvable problem of philosophy.

The subjects of the book are: the relations between philosophy and rhetoric, the speaker and the addressee of philosophical arguments, the subordination of logic to rhetoric in philosophy and the philosophical problem of self-deception.
This work, unburdened with philosophers’ jargon, fits well in the current critical debate about the relevance of pragmatic features of the concepts of subjectivity and truth.
Connecting Grammaticalisation
Authors: Nørgård-Sørensen Jens , Heltoft Lars , Schøsler Lene 
Published: December 2013

This monograph presents a view on grammaticalisation radically different from standard views centering around the cline of grammaticality. Grammar is seen as a complex sign system, and, as a consequence, grammatical change always comprises semantic change. What unites morphology, topology (word order), constructional syntax and other grammatical subsystems is their paradigmatic organisation. The traditional concept of an inflexional paradigm is generalised as the structuring principle of grammar. Grammatical change involves paradigmatic restructuring, and in the process of grammatical change morphological, topological and constructional paradigms often connect to form complex paradigms. The book introduces the concept of connecting grammaticalisation to describe the formation, restructuring and dismantling of such complex paradigms. Drawing primarily on data from Germanic, Romance and Slavic languages, the book offers both a broad general discussion of theoretical issues (part one) and three case studies (part two).
As of March 2017, this e-book is freely available, thanks to the support of libraries working with Knowledge Unlatched.
Essays in the History of Linguistics
Authors: Koerner E.F.K. 
Published: December 2013

The present volume follows the author's tradition of bringing together at certain intervals selections of articles which more often than not had previously been published in not easily accessible places, or which had not been published before. These papers do not typically represent mere reprints but in most instances thoroughly revised versions.
This volume contains twelve articles organized under three headings, "Programmatic Papers in the History of Linguistics", "Studies in Linguistic Historiography", and "Sketches historiographical and (auto)biographical", plus as an appendix a complete list of Zellig Harris' writings as an illustration of Koerner's penchant for and belief in the importance of good bibliographies as a basis for historical research. While the first two sections, which take up the bulk of the volume, either show the author as an historian engagé or demonstrate his work as a historiographer of 19th and 20th century linguistics, the third section is much shorter and less heavy going. Indexes of Biographical Names and of Subjects, Terms & Languages round out the volume, which also contains a number of portraits of linguists and other illustrations.
Infestation and Pathological Alterations by Ergasilus sarsi (Copepoda) on the Tanganyika Killifish from Africa
Authors: Kilian Esmari , Avenant-Oldewage Annemariè 
Published: December 2013

Abstract
A total of 204 Ergasilus sarsi, a copepod, were collected from Tanganyika Killifish Lamprichthys tanganicanus in Lake Tanganyika during March 2010. The prevalence was 86.40%, the mean intensity was 7.56, and the mean abundance was 6.38. Only 27 of the fish were infested, and the highest infestation on one fish was 29. Proliferation of mucus cells and lamellar fusion occurred. Haemorrhage due to blood vessel compression was noted. This is the first record of E. sarsi from Tanganyika Killifish. This study is also the first to provide a description of the pathological alterations caused by E. sarsi.
Received April 2, 2013; accepted May 31, 2013
Fish Processing Facilities: New Challenge to Marine Biosecurity in Canada
Authors: Price M. H. H. , Morton A. , Eriksson J. G. , Volpe J. P. 
Published: December 2013

Abstract
The transmission of pathogens is a common consequence of animal food production. Marine salmon farms and their processing facilities can serve as sources of virulent fish pathogens; our study is the first to confirm the broadcast of a live fish pathogen from a farmed salmon processing facility into the marine waters of Canada's Pacific coast. We found live salmon lice Lepeophtheirus salmonis, mucus, and fish tissue in effluent from the processing facility. Sea lice transmitted from this source may pose a threat to wild salmon populations, and the release of untreated offal, including blood water, is of considerable concern. Further research is needed to quantify the extent to which processing facilities release sea lice and to determine whether more virulent fish pathogens are present in effluent. These data underscore the need for fish farming nations to develop mandatory biosecurity programs to ensure that farmed salmon processing facilities will prevent the broadcast of infectious fish pathogens into wild fish habitat.
Received April 26, 2012; accepted September 7, 2013
CrossMap: a versatile tool for coordinate conversion between genome assemblies
Authors: Zhao Hao , Sun Zhifu , Wang Jing , Huang Haojie , Kocher Jean-Pierre , Wang Liguo 
Published: December 2013

Abstract
Motivation: Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results that have been analyzed according to old assemblies to newer versions, or vice versa, to facilitate meta-analysis, direct comparison, data integration and visualization. Several useful conversion tools can convert genome interval files in browser extensible data or general feature format, but none have the functionality to convert files in sequence alignment map or BigWig format. This is a significant gap in computational genomics tools, as these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, chromatin immunoprecipitation sequencing, DNA-seq, etc.
Results: Here we developed CrossMap, a versatile and efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.
Availability and implementation: CrossMap is written in Python and C. Source code and a comprehensive user’s manual are freely available at: http://crossmap.sourceforge.net/.
Contact: Kocher.JeanPierre@mayo.edu or wang.liguo@mayo.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Procedure-specific Risk Factor Analysis for the Development of Severe Postoperative Pain
Authors: Gerbershagen Hans J. , Pogatzki-Zahn Esther , Aduckathil Sanjay , Peelen Linda M. , Kappen Teus H. , van Wijck Albert J. M. , Kalkman Cor J. , Meissner Winfried 
Published: December 2013

Abstract

Background:
Many studies have analyzed risk factors for the development of severe postoperative pain with contradictory results. To date, the association of risk factors with postoperative pain intensity among different surgical procedures has not been studied and compared.

Methods:
The authors selected precisely defined surgical groups (at least 150 patients each) from prospectively collected perioperative data from 105 German hospitals (2004–2010). The association of age, sex, and preoperative chronic pain intensity with worst postoperative pain intensity was studied with multiple linear and logistic regression analyses. Pooled data of the selected surgeries were studied with random-effect analysis.

Results:
Thirty surgical procedures with a total number of 22,963 patients were compared. In each surgical procedure, preoperative chronic pain intensity and younger age were associated with higher postoperative pain intensity. A linear decline of postoperative pain with age was found. Females reported more severe pain in 21 of 23 surgeries. Analysis of pooled surgical groups indicated that postoperative pain decreased by 0.28 points (95% CI, 0.26 to 0.31) on the numeric rating scale (0 to 10) per decade age increase and postoperative pain increased by 0.14 points (95% CI, 0.13 to 0.15) for each higher score on the preoperative chronic pain scale. Females reported 0.29 points (95% CI, 0.22 to 0.37) higher pain intensity.

Conclusions:
Independent of the type and extent of surgery, preoperative chronic pain and younger age were associated with higher postoperative pain. Females consistently reported slightly higher pain scores regardless of the type of surgery. The clinical significance of this small sex difference has to be analyzed in future studies.
The Accuracy of Transit Time Flow Measurement in Predicting Graft Patency after Coronary Artery Bypass Grafting
Authors: Walker Patrick F. , Daniel William T. , Moss Emmanuel , Thourani Vinod H. , Kilgo Patrick , Liberman Henry A. , Devireddy Chandan , Guyton Robert A. , Puskas John D. , Halkos Michael E. 
Published: December 2013

Objective Transit time flow measurement (TTFM) is a method used to assess intraoperative blood flow after vascular anastomoses. Angiography represents the criterion standard for the assessment of graft patency after coronary artery bypass grafting (CABG). The purpose of this study was to compare flow measurements from TTFM to diagnostic angiography. Methods From October 9, 2009, to April 30, 2012, a total of 259 patients underwent robotic-assisted CABG procedures at a single institution. Of these, 160 patients had both TTFM and either intraoperative or postoperative angiography of the left internal mammary artery to the left anterior descending coronary artery graft. Transit time flow measurements were obtained after completion of the anastomosis and after administration of protamine before chest closure. Transit time flow measurement assessment included pulsatility index, diastolic fraction, and flow (milliliters per minute). Angiograms were graded according to the Fitzgibbon criteria. The patients were grouped according to angiographic findings, with perfect grafts defined as FitzGibbon A and problematic grafts defined as either Fitzgibbon B or O. Results Overall, there were 152 (95%) of 160 angiographically perfect grafts (FitzGibbon A). Of the eight problematic grafts, five were occluded (Fitzgibbon O) and three had significant flow-limiting lesions (FitzGibbon B). Two patients had intraoperative graft revision after completion angiography, one had redo CABG during the same hospitalization, and five were treated with percutaneous coronary intervention. A significant difference was seen in mean ± SD flow (34.3 ± 16.8 mL/min vs 23.9 ± 12.5 mL/min, P = 0.033) between patent and nonpatent grafts but not in pulsatility index (1.98 ± 0.76 vs 1.65 ± 0.48, P = 0.16) or diastolic fraction (73.5% ± 8.45% vs 70.9% ± 6.15%, P = 0.13). Conclusions Although TTFM can be a useful tool for graft assessment after CABG, false negatives can occur. Angiography remains the criterion standard to assess graft patency and quality of the anastomosis after CABG.
How Does the Surgeon's Experience of Abdominal Operations Influence the Learning Curves for Robot-Assisted Vascular Anastomosis?
Authors: Soga Shingo , Watanabe Go , Ishikawa Norihiko , Kimura Keiichi , Oda Makoto 
Published: December 2013

Objective Endoscopic vascular anastomosis of abdominal aortic aneurysms is rarely performed and requires standardization. Here, we examined the impact of the surgeon's experience of abdominal aortic aneurysm surgery on the learning curve for robot-assisted endoscopic vascular anastomosis. Methods Three vascular surgeons with more than 10 years’ experience (group A), three vascular surgeons with less than 10 years’ experience (group B), and three medical students with no experience (group C) of performing vascular surgery used the da Vinci surgical system to anastomose 8-mm–diameter vascular prostheses in an end-to-end manner with continuous 5–0 Prolene sutures. The procedure was performed five times by each participant. Outcomes were anastomosis time, number of actions, visual score, and pressure test. Snapping of the prolene thread was recorded as a procedural failure. Results Procedural failure occurred only in group C (3/15 trials, 20%; P < 0.0001). Learning curves were apparent in all three groups for anastomosis time and in groups A and C for the number of actions. Between trials 1 and 5, learning curves were apparent in all three groups for anastomosis time and in groups A and C for the number of actions but were not apparent for leakage or visual score in any group. Visual score and leakage were not significantly different among the three groups in each trial ( P = 0.10 and P = 0.45, respectively). Conclusions By using the da Vinci surgical system, experienced vascular surgeons and surgically naive students showed marked improvements in vascular anastomosis techniques with a short period of training.