bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of thresholds for dichotomizing DNA methylation data
Authors: Liu Yihua , Ji Yuan , Qiu Peng 
Published: June 2013

Abstract
DNA methylation plays an important role in many biological processes by regulating gene expression. It is commonly accepted that turning on the DNA methylation leads to silencing of the expression of the corresponding genes. While methylation is often described as a binary on-off signal, it is typically measured using beta values derived from either microarray or sequencing technologies, which takes continuous values between 0 and 1. If we would like to interpret methylation in a binary fashion, appropriate thresholds are needed to dichotomize the continuous measurements. In this paper, we use data from The Cancer Genome Atlas project. For a total of 992 samples across five cancer types, both methylation and gene expression data are available. A bivariate extension of the StepMiner algorithm is used to identify thresholds for dichotomizing both methylation and expression data. Hypergeometric test is applied to identify CpG sites whose methylation status is significantly associated to silencing of the expression of their corresponding genes. The test is performed on either all five cancer types together or individual cancer types separately. We notice that the appropriate thresholds vary across different CpG sites. In addition, the negative association between methylation and expression is highly tissue specific.
Origins of increased airway smooth muscle mass in asthma
Authors: Berair Rachid , Saunders Ruth , Brightling Christopher E 
Published: June 2013

Abstract
Asthma is characterized by both chronic inflammation and airway remodeling. Remodeling - the structural changes seen in asthmatic airways - is pivotal in the pathogenesis of the disease. Although significant advances have been made recently in understanding the different aspects of airway remodeling, the exact biology governing these changes remains poorly understood. There is broad agreement that, in asthma, increased airway smooth muscle mass, in part due to smooth muscle hyperplasia, is a very significant component of airway remodeling. However, significant debate persists on the origins of these airway smooth muscle cells. In this review article we will explore the natural history of airway remodeling in asthma and we will discuss the possible contribution of progenitors, stem cells and epithelial cells in mesenchymal cell changes, namely airway smooth muscle hyperplasia seen in the asthmatic airways.
Solitary myofibroma of the sigmoid colon: case report and review of the literature
Authors: Kim Mi-Jung , Lee Suk Hee , Youk Eui Gon , Lee Sojin , Choi Joon Hyuk , Cho Kyung-Ja 
Published: June 2013

Abstract
A 58-year-old woman presented with a solitary myofibroma that arose in the sigmoid colon. Computed tomography revealed a highly enhanced intramural mass (1.3-cm maximum diameter) in the proximal sigmoid colon. Histologically, the tumor exhibited a biphasic growth pattern, which comprised haphazardly arranged, interwoven fascicles of plump, myoid-appearing spindle cells with elongated nuclei and abundant eosinophilic cytoplasm, and more cellular areas of primitive-appearing polygonal cells that were arranged in a hemangiopericytomatous pattern. The tumor cells were positive for smooth muscle actin (SMA), and negative for desmin, h-caldesmon, CD34, cytokeratin, S100 protein, and CD117. The Ki-67 labeling index was not high (up to 7%). Based on these histologic and immunohistochemical features, our patient was diagnosed with a myofibroma of the sigmoid colon. The presence of solitary myofibroma in the intestine of an adult requires attention to avoid misdiagnosis as a more aggressive mesenchymal tumor.

Virtual Slides

The virtual silde(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2096403796957687
The binding characteristics of isoniazid with copper–zinc superoxide dismutase and its effect on enzymatic activity
Authors: Du Nana , Sheng Liangquan , Liu Zhaodi , Hu Xiaojuan , Xu Huajie , Chen Shuisheng 
Published: June 2013

Abstract

Background
Isoniazid (INH) is front-line anti-tuberculosis (TB) drugs, which are usually prescribed to TB patients for a total period of 6 months. Antituberculosis drug-induced hepatotoxicity (ATDH) is a serious adverse reaction of TB treatment. It is reported that INH-induced hepatotoxicity is associated with oxidative stress. Superoxide dismutase (SOD, EC 1.15.1.1) is the key enzyme for the protection of oxidative stress, which catalyzes the removal of superoxide radical anion, thereby raising the need to better understand the interaction between INH and SOD.

Results
The experimental results showed that the fluorescence intensity of Cu/Zn-SOD regularly decreased owing to form a 1:1 INH-SOD complex. According to the corresponding association constants (K
SV) between INH and SOD obtained from Stern–Volmer plot, it is shown that values of K
A are 1.01 × 104, 5.31 × 103, 3.33 × 103, 2.20 × 103 L · mol−1 at four different temperatures, respectively. The binding constants, binding sites and the corresponding thermodynamic parameters (Δ
H, Δ
G and Δ
S) were calculated. A value of 3.93 nm for the average distance between INH and chromophore of Cu/Zn-SOD was derived from Förster theory of non-radiation energy transfer. The conformational investigation showed that the presence of INH resulted in the microenvironment and conformational changes of Cu/Zn-SOD. In addition, Effects of INH on superoxide dismutase activity was examined.

Conclusions
The results show that the hydrogen bonding and van der Waals forces play major roles in stabilizing the 1:1 INH-SOD complex. After addition of INH during the range of the experiment, the conformation and microenvironment of Cu/Zn-SOD are changed, but the activity of Cu/Zn-SOD is not changed.
In vitro and in vivo properties of CD133 expressing cells from human lung cancer cell lines
Authors: Wang Ping , Suo Zhenhe , Wang Mengyu , Høifødt Hanne K , Fodstad Øystein , Gaudernack Gustav , Kvalheim Gunnar 
Published: June 2013

Abstract

Background
Tumor development is recently hypothesized to depend on a rare cell population with stem cell properties, such cells are called cancer stem cells (CSCs) or tumor-initiating cells (TICs). From various cancer tissues or cancer cell lines, CD133 expressing cells were found to define a unique CSC/TIC phenotype. To study whether that also could be the case in lung cancer, we examined different lung cancer cell lines for CD133 expression.

Results
Among the 4 cell lines studied, only the cell line LC-42 expressed CD133. Therefore, LC-42 was further characterized and studied with special emphasis on identifying the presence of CD133+ CSCs/TICs. FACS sorted CD133high and CD133dim subpopulations from LC-42 showed no differences in soft agar colony-forming capacity and spheres-forming capacity in serum-free cultures. LC-42 cells contained Side Population (SP), and only SP cells were able to form spheres. Furthermore, Nanog expression was significantly higher in SP than in non-SP. However, no difference was observed of CD133 expression in SP and non-SP. When CD133high and CD133dim cells were serially xeno-transplanted in NOD/SCID mice, both formed tumours similar to their parental LC-42 cells. There were no expression differences for NANOG, OCT4 and SOX2 examined immunohistochemically in the xenografts from both cell fractions.

Conclusion
Our data do not show a difference in tumorigenic potential of CD133high and CD133dim cells with respect to any of the parameters analyzed in vitro and in viv o, suggesting that CD133 expression is not restricted to cancer-initiating cells in the human lung cancer cell line LC-42.
Highly Crosslinkable and Proton-conducting Polyelectrolytes of Pore-filling Membranes for Proton Exchange Membrane Fuel Cells
Authors: Park Jin-Soo , Choi Young-Woo 
Published: June 2013

Abstract
In this study, new polyelectrolytes with highly crosslinkable and proton-conducting properties for pore filling membranes with no external solvents were introduced. It was found that the liquid monomers show more facile copolymerization as well as crosslinking than solid monomers dissolved in a solvent. Moreover, the membranes exhibited better durability due to extensive crosslinking and proton conductivity due to facile copolymerization. The resulting membrane exhibits proton conductivity of 0.09 S cm−1 at room temperature with stable fuel cell operation for 1000 h.
A One-pot Preparation of 1,3-Diarylisobenzofuran
Authors: Hamura Toshiyuki , Nakayama Ryosuke 
Published: June 2013

Abstract
A simple, practical, and efficient method for one-pot synthesis of symmetric and unsymmetrical 1,3-diarylisobenzofurans has been developed by sequential reactions of methyl 2-formylbenzoate with two identical or different aryl metal species.
Basicity of N-Terminal Amine in ATCUN Peptide Regulates Stability Constant of Albumin-like Cu2+ Complex
Authors: Miyamoto Takaaki , Kamino Shinichiro , Odani Akira , Hiromura Makoto , Enomoto Shuichi 
Published: June 2013

Abstract
We quantitatively investigated the coordination ability of ATCUN peptides possessing various amino acid residues on the N-terminal side of the third histidine, toward Cu2+. We discovered that the stability of the Cu2+–ATCUN complex was governed by the acidity of the N-terminal amino nitrogen in the peptides.
Cold Crystallization in Bis[1-(3-methylphenyl)iminomethylnaphthalen-2-olato]nickel(II) Studied by Thermal Analysis and X-ray Diffraction
Authors: Iwase Katsunori , Houjou Hirohiko , Yamamura Yasuhisa , Saito Kazuya 
Published: June 2013

Abstract
Bis[1-(3-methylphenyl)iminomethylnaphthalen-2-olato]nickel(II) was synthesized to see a potential use of this type of compounds as heat-storage materials utilizing cold crystallization. Its thermal, structural, and energetic properties were investigated by thermal analysis, X-ray diffraction, and DFT calculation. Some principles in designing complexes for this purpose are deduced.
Discrimination of Xylose O-Glycosylation Sites in Mammalian Proteins
Authors: Etchuya Kenji , Nambu Ryohei , Mukai Yuri 
Published: June 2013

Abstract
A method for discriminating xylose (Xyl) O-glycosylation sites from other sugar modification sites was proposed. Xyl modification sites were detected by position-specific scoring matrix (PSSM) with 97.9 and 87.5% success rates in self-consistency and 5-fold cross-validation test, respectively. Glycosyltransferases concerned with Xyl modification were thought to recognize amino acid sequences around modification sites.
In Situ Detection of Liver Cancer Biomarkers with Atomic Force Microscopy at a Single-molecule Level
Authors: Tang Bochong , Li Min , Zhang Xiao , Wang Jiaojiao , Xie Peng , Zhao Yuliang , Wei Zhongqing 
Published: June 2013

Abstract
α-Fetoprotein (AFP), a surveillance biomarker of liver cancer, was directly detected via immunoassay at a single-molecule level using in situ atomic force microscopy (AFM). AFM size measurements confirmed the successful capture of single AFP molecules by monoclonal antibody molecules on a one-to-one basis.
Child Work in Agriculture in West Bengal, India: Assessment of Musculoskeletal Disorders and Occupational Health Problems
Authors: Das Banibrata , Ghosh Tirthankar , Gangopadhyay Somnath 
Published: June 2013

Child Work in Agriculture in West Bengal, India: Assessment of Musculoskeletal Disorders and Occupational Health Problems: Banibrata DAS, et al. Department of Physiology, South Calcutta Girls' College University of Calcutta, India—ObjectiveChildren are universally considered to be the most important asset for any nation. The main aims of the present study were 1) to investigate the causation of discomfort related to working postures 2) to assess the physiological strain among the child farmers and 3) to assess the thermal stress during work in an agricultural field.MethodsFor this study, 120 child agricultural workers and 120 control subjects aged 10−16 years were selected randomly, and a detailed posture analysis was performed among them by REBA and OWAS methods. The Modified Nordic Questionnaire was applied to assess the discomfort felt among both groups of workers. Physiological assessment of workload was carried out by recording the heart rate and blood pressure of the workers prior to work and just after work in the field.ResultsChild agricultural workers suffered from pain especially in the low back (98%), knees (88%), hands (82%), shoulder (77%) and neck (68%). Among the agricultural activities in potato cultivation, the child potato workers, felt discomfort during spading (99%), sprinkling water (90%) and picking crops (87%). The post‐activity heart rate of the child agricultural workers was 170.1 beats/min, whereas the systolic and diastolic blood pressures were 129.0 and 67.0 mm/Hg respectively.ConclusionsMost of the agricultural activities in potato cultivation were strenuous ones that affect the children, who suffered from acute pain and discomfort for a long period of time, which mainly hampers and restricts their education.
Work‐to‐family Conflict and Family‐to‐work Conflict among Japanese Dual‐earner Couples with Preschool Children: A Spillover‐Crossover Perspective
Authors: Shimazu Akihito , Kubota Kazumi , Bakker Arnold , Demerouti Eva , Shimada Kyoko , Kawakami Norito 
Published: June 2013

Work‐to‐family Conflict and Family‐towork Conflict among Japanese Dual‐earner Couples with Preschool Children: A Spillover‐Crossover Perspective: Akihito SHIMAZU, et al. Department of Mental Health, The University of Tokyo Graduate School of Medicine, Japan—ObjectivesThis study among Japanese dual‐earner couples examined the independent and combined associations of work‐tofamily conflict (WFC) and family‐to‐work conflict (FWC) with psychological health of employees and their partners and the relationship quality between partners.MethodsThe matched responses of 895 couples were analyzed with logistic regression analysis to examine whether there were differences among the four work‐family conflict groups (i.e., no conflict, WFC, FWC and both conflicts groups) in terms of own psychological distress, social undermining (i.e., negative behaviors directed toward the target person) reported by partners and partner's psychological distress. The no conflicts group was used as the reference group.ResultsThe both conflicts group had the highest odds ratios for own psychological distress and social undermining towards the partner for both genders. In addition, for husbands, the both conflicts group had the highest odds ratio for partner's psychological distress, whereas for wives, it did not.ConclusionsDual experiences of WFC and FWC have adverse associations with psychological health of employees and relationship quality between partners of both genders. In addition, dual experiences in husbands have an adverse association with psychological health of their partners (i.e., wives), whereas this is not the case for wives.
Three-Dimensional Nanoarchitectured Transparent Conducting Oxides: Synthesis, Characterization and Photovoltaic Applications
Authors: Yang Zhenzhen , Xu Tao 
Published: June 2013

AbstractThe photovoltaic materials in solar cells take multiple tasks including absorbing lights, separating the light-induced electron-hole pairs, and consequently transport charges to the corresponding metallic electrodes. These tasks, however, are often mutually conflicting. In particular, a thick PV layer is desired to absorb enough light for creating sufficient light-induced charges, while a thin PV layer is also desired to shorten the charge transport path length insider the PV layer in order to suppress recombination. Using dye-sensitized solar cells as an exploratory platform, this dilemma is mitigated using a non-traditional 3-dimensional (3-D) highly doped fluorinated SnO2 (FTO, core)-TiO2(shell) nanostructured photoanodes. The FTO core serves as conductive core for low-resistance and drift-assisted electron extraction. The thin, conformal and low-doped TiO2 shell layer is coated by atomic layer deposition, which provides a large area for anchoring dyes and maintains a large resistance against recombination.
Tip-Sample Forces in Atomic Force Microscopy: Interplay between Theory and Experiment
Authors: Belikov Sergey , Alexander John , Wall Craig , Magonov Sergei 
Published: June 2013

ABSTRACTSeveral examples of Atomic Force Microscopy imaging in the oscillatory resonant and non-resonant modes are analyzed with a theoretical description of tip-sample force interactions. The problems of high-resolution imaging and compositional mapping of heterogeneous polymers are considered. The interplay with theory helps the experiment optimization and rational understanding of the image contrast.
Behavior of Magnetic Domains in Single Magnetic Nanowire with Shallow Trench along Length Direction Observed by Magnetic Force Microscopy
Authors: Okuda Mitsunobu , Miyamoto Yasuyoshi , Miyashita Eiichi , Hayashi Naoto 
Published: June 2013

ABSTRACTWe have proposed new magnetic memories using parallel-aligned nanowires without mechanical moving parts, in order to achieve the ultra high transfer rate of more than 144 Gbps for Super Hi-Vision TV. In the magnetic memory using nanowires, the data are stored as the magnetic domains with up or down magnetization in magnetic nanowires, and the domains are shifted quite faster by applying optimum current along the nanowire direction for data writing and reading purpose. Since the electric circuits and the insulation space between the neighbor nanowires are necessary for moving the magnetic domain walls, the areal recording density is essentially reduced as compared with that of conventional hard disk drives. In this study, in order to increase the areal recording density of magnetic nanowire memory, we have tried to act one magnetic nanowire as the virtual multiple data tracks. The shallow scratched trench was introduced using scanning probe microscopy along the length direction on the surface of a single nanowire to form multiple internal tracks, and we have succeeded in realizing a couple of virtual tracks states.
Hybrid SWCNT - NiO Composites for Supercapacitor Applications
Authors: Alston Jeffrey R. , Brokaw Dylan , Overson Colton , Schmedake Thomas A. , Poler Jordan C. 
Published: June 2013

ABSTRACTSupercapacitor devices promise to be an effective means of storing energy, and delivering power for personal electronics, remote sensors, and transportation.1, 2 Rare earth metals, such as ruthenium, have been used and report high value of capacitance, specific power, and energy.4 Nevertheless, the rarity of such metals prevent their practical use. In this study we utilize an earth-abundant nickel and a controlled microwave synthesis to create nickel oxide (NiO) with an optimal nanostructure for capacitance. To surpass the lofty series resistance associated with metal oxides such as NiO, we exploit the conductive properties of single and multi-walled carbon nanotubes. The carbon nanotubes and NiO can benefit from the presence of each other by preventing unnecessary aggregation.
Reviews
Authors: Warkentin Germaine , Stevens Paul , Gatrell Simon , Reibetanz  , Rosenberg Aubrey 
Published: June 2013

Marjorie O'Rourke Boyle, Petrarch's Genius: Pentimento and Prophecy, reviewed by Germaine Warkentin Jeffrey Knapp, An Empire Nowhere: England, America, and Literature From 'Utopia' to 'The Tempest' reviewed by ___________ Pamela Dalziel, ed., Thomas Hardy: The Excluded and Collaborative Stories, reviewed by Simon Gatrell David Marr, Patrick White: A Life, reviewed by J. M. Reibetanz Raymond Trousson, Jean-Jacques Rousseau. II. Le deuil éclatant du bonheur, reviewed by Aubrey Rosenberg
La construction sociale d'un territoire professionnel : les agents artistiques
Authors: Naudier Delphine 
Published: June 2013

Qu’ils soient qualifiés d’impresarios ou d’agents artistiques, ces acteurs des mondes de l’art occupent depuis la fin du XIX e siècle une fonction d’intermédiaires sur le marché du travail artistique. Il s’agit de montrer comment les agents artistiques ont progressivement construit leur territoire professionnel, oscillant entre absence de règlementation, encadrement et libéralisation de l’activité. D’abord peu encadrée, discréditée en raison de la présomption d’escroquerie qui pèse sur elle, la profession est progressivement contrôlée par les autorités préfectorales et municipales. La construction sociale de la profession s’appuie sur un travail de moralisation et d’encadrement de l’activité qui, après avoir obtenu une dérogation d’exercice alors que les bureaux de placement payants étaient supprimés, aboutit ensuite à sa légalisation par la loi de décembre 1969. Enfin, à partir de 2004, une autre phase est amorcée qui aboutit en 2010, avec l’application de la directive Bolkenstein, à la libéralisation de la profession. De l’activité de placement à celle de la représentation des intérêts professionnels qui élargit la palette de leurs prérogatives, la légalisation de l’activité s’est construite à la croisée des luttes syndicales des artistes et de la structuration interne de ce territoire professionnel très hétérogène et hiérarchisé.
Le droit à l'espace : l'exemple des Gens du voyage en Île-de-France
Authors: Desbois Jérôme 
Published: June 2013

Le mode de vie singulier des Gens du voyage – environ 50 000 personnes en Île-de-France – ainsi que leur habitat spécifique, la caravane, sont connus, pourtant rien n’est fait pour permettre qu’ils soient respectés. Dans cet article Jérôme Desbois propose de présenter la situation des Gens du voyage en Île-de-France, en pointant les difficultés et obstacles administratifs qu’ils rencontrent pour accéder à un habitat décent. L’auteur interroge le rôle que jouent ces obstacles administratifs dans le parcours du combattant que constitue la satisfaction, par les populations nomades, d’un droit à l’espace : les outils administratifs mis en place ne sont-ils pas, purement et simplement, à l’origine d’une stigmatisation et relégation institutionnalisées de ces populations, et en particulier des Tsiganes, en Île-de-France ?
« L'État nous quitte »
Authors: Bulle Sylvaine 
Published: June 2013

Pendant 6 mois entre l’été 2011 et l’hiver 2012, un large mouvement de contestation populaire israélien a pris corps dans les villes, bénéficiant de relais dans l’opinion publique et l’espace médiatique et a ébranlé la vie politique israélienne. Le soulèvement intervenu dans le contexte des « printemps des peuples » qui se prolonge aujourd’hui par des actions collectives plus ou moins robustes (campements, tribunal populaire, assemblée du peuple) doit pouvoir être lu à partir de visées sociologiques et politiques renvoyant à la question économique sociale et culturelle en Israël. Celle-ci est en tout état de cause le reflet du recul de l’État social qui était au cœur du projet sioniste. Dans cet article, l’auteure porte l’attention sur cette question de deux ordres : l’analyse des justifications critiques qui ont pu permettre, le temps d’une révolte de dénoncer la réalité et la façon dont les controverses (notamment dans le domaine du logement) sont portées en public.
Le squat, un droit à la ville en actes
Authors: Aguilera Thomas , Bouillon Florence 
Published: June 2013

Le squat est le plus souvent appréhendé par les sciences sociales sous l’angle des mobilisations collectives. L’idée de « droit à la ville » est au cœur de la rhétorique des squatteurs politiques et de leurs répertoires d’action. Les auteurs reviennent, dans cet article, sur cette hypothèse en mobilisant des résultats d’enquêtes réalisées à Paris, à Marseille et à Madrid. Il s’agira alors d’évoquer un tout autre visage du squat, souvent négligé car plus discret : celui des squats de « pauvreté », occupés par les citadins les plus démunis et disqualifiés.