bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trastuzumab resistance induces EMT to transform HER2+ PTEN− to a triple negative breast cancer that requires unique treatment options
Authors: Burnett Joseph P. , Korkaya Hasan , Ouzounova Maria D. , Jiang Hui , Conley Sarah J. , Newman Bryan W. , Sun Lichao , Connarn Jamie N. , Chen Ching-Shih , Zhang Ning , Wicha Max S. , Sun Duxin 
Published: November 2015

AbstractAlthough trastuzumab is an effective treatment in early stage HER2+ breast cancer the majority of advanced HER2+ breast cancers develop trastuzumab resistance, especially in the 40% of breast cancers with loss of PTEN. However, HER2+ breast cancer patients continue to receive trastuzumab regardless PTEN status and the consequence of therapy in these patients is unknown. We demonstrate that continued use of trastuzumab in HER2+ cells with loss of PTEN induces the epithelial-mesenchymal transition (EMT) and transform HER2+ to a triple negative breast cancer. These transformed cells exhibited mesenchymal morphology and gene expression markers, while parent HER2+ cells showed epithelial morphology and markers. The transformed cells exhibited loss of dependence on ERBB family signaling (such as HER2, HER3, HER4, BTC, HRG, EGF) and reduced estrogen and progesterone receptors. Continued use of trastuzumab in HER2+ PTEN− cells increased the frequency of cancer stem cells (CSCs) and metastasis potential. Strikingly, parental HER2+ cells and transformed resistant cells respond to treatment differently. Transformed resistant cells were sensitive to chemical probe (sulforaphane) through inhibition of IL-6/STAT3/NF-κB positive feedback loop whereas parental HER2+ cells did not respond. This data suggests that trastuzumab resistance in HER2+ PTEN− breast cancer induces EMT and subtype switching, which requires unique treatment options.
Optical forces in nanorod metamaterial
Authors: Bogdanov Andrey A. , Shalin Alexander S. , Ginzburg Pavel 
Published: October 2015

AbstractOptomechanical manipulation of micro and nano-scale objects with laser beams finds use in a large span of multidisciplinary applications. Auxiliary nanostructuring could substantially improve performances of classical optical tweezers by means of spatial localization of objects and intensity required for trapping. Here we investigate a three-dimensional nanorod metamaterial platform, serving as an auxiliary tool for the optical manipulation, able to support and control near-field interactions and generate both steep and flat optical potential profiles. It was shown that the ‘topological transition’ from the elliptic to hyperbolic dispersion regime of the metamaterial, usually having a significant impact on various light-matter interaction processes, does not strongly affect the distribution of optical forces in the metamaterial. This effect is explained by the predominant near-fields contributions of the nanostructure to optomechanical interactions. Semi-analytical model, approximating the finite size nanoparticle by a point dipole and neglecting the mutual re-scattering between the particle and nanorod array, was found to be in a good agreement with full-wave numerical simulation. In-plane (perpendicular to the rods) trapping regime, saddle equilibrium points and optical puling forces (directed along the rods towards the light source), acting on a particle situated inside or at the nearby the metamaterial, were found.
Electronic Properties of Fluoride and Half–fluoride Superlattices KZnF3/KAgF3 and SrTiO3/KAgF3
Authors: Yang Xiaoping , Su Haibin 
Published: October 2015

AbstractWe present the formation of cupratelike electronic structures in KAgF3–related superlattices resulted from the confinement together with structural chemical modification by using the generalized gradient approximation augmented with maximally localized Wannier functions analysis. Strong antiferromagnetic coupling found in bulk KAgF3 is held in purely–fluoride KZnF3/KAgF3. Under 4% in–plane compression strain, its Fermi surface shape breaks away from the edge of electron pocket and resembles that of La2CuO4. While within half–fluoride SrTiO3/KAgF3, out–of–plane electronic reconstruction results in electron doping of AgF2 plane and antiferromagnetic state instability and the Fermi surface shape presents considerable similarity to that in HgBaCuO4. These results shed light on two dimensional antiferromagnetic precursors of a new AgII family of high–temperature superconductors.
Optimizing Multiple Analyte Injections in Surface Plasmon Resonance Biosensors with Analytes having Different Refractive Index Increments
Authors: Mehand Massinissa Si , Srinivasan Bala , De Crescenzo Gregory 
Published: October 2015

AbstractSurface plasmon resonance-based biosensors have been successfully applied to the study of the interactions between macromolecules and small molecular weight compounds. In an effort to increase the throughput of these SPR-based experiments, we have already proposed to inject multiple compounds simultaneously over the same surface. When specifically applied to small molecular weight compounds, such a strategy would however require prior knowledge of the refractive index increment of each compound in order to correctly interpret the recorded signal. An additional experiment is typically required to obtain this information. In this manuscript, we show that through the introduction of an additional global parameter corresponding to the ratio of the saturating signals associated with each molecule, the kinetic parameters could be identified with similar confidence intervals without any other experimentation.
Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture
Authors: Wu Linkun , Wang Juanying , Huang Weimin , Wu Hongmiao , Chen Jun , Yang Yanqiu , Zhang Zhongyi , Lin Wenxiong 
Published: October 2015

AbstractUnder consecutive monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during monoculture. Prolonged monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.
The Akt-mTOR axis is a pivotal regulator of eccentric hypertrophy during volume overload
Authors: Ikeda Masataka , Ide Tomomi , Fujino Takeo , Matsuo Yuka , Arai Shinobu , Saku Keita , Kakino Takamori , Oga Yasuhiro , Nishizaki Akiko , Sunagawa Kenji 
Published: October 2015

AbstractThe heart has two major modalities of hypertrophy in response to hemodynamic loads: concentric and eccentric hypertrophy caused by pressure and volume overload (VO), respectively. However, the molecular mechanism of eccentric hypertrophy remains poorly understood. Here we demonstrate that the Akt-mammalian target of rapamycin (mTOR) axis is a pivotal regulator of eccentric hypertrophy during VO. While mTOR in the heart was activated in a left ventricular end-diastolic pressure (LVEDP)-dependent manner, mTOR inhibition suppressed eccentric hypertrophy and induced cardiac atrophy even under VO. Notably, Akt was ubiquitinated and phosphorylated in response to VO and blocking the recruitment of Akt to the membrane completely abolished mTOR activation. Various growth factors were upregulated during VO, suggesting that these might be involved in Akt-mTOR activation. Furthermore, the rate of eccentric hypertrophy progression was proportional to mTOR activity, which allowed accurate estimation of eccentric hypertrophy by time-integration of mTOR activity. These results suggested that the Akt-mTOR axis plays a pivotal role in eccentric hypertrophy and mTOR activity quantitatively determines the rate of eccentric hypertrophy progression. As eccentric hypertrophy is an inherent system of the heart for regulating cardiac output and LVEDP, our findings provide a new mechanistic insight into the adaptive mechanism of the heart.
Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation
Authors: Zhang Hailei , Gu Zongying , Wu Qiao , Yang Lifeng , Liu Caifeng , Ma Hong , Xia Yiji , Ge Xiaochun 
Published: October 2015

AbstractPoly(ADP-ribosyl)ation is a reversible post-translational modification of proteins, characterized by the addition of poly(ADP-ribose) (PAR) to proteins by poly(ADP-ribose) polymerase (PARP) and removal of PAR by poly(ADP-ribose) glycohydrolase (PARG). Three PARPs and two PARGs have been found in Arabidopsis, but their respective roles are not fully understood. In this study, the functions of each PARP and PARG in DNA repair were analyzed based on their mutant phenotypes under genotoxic stresses. Double or triple mutant analysis revealed that PARP1 and PARP2, but not PARP3, play a similar but not critical role in DNA repair in Arabidopsis seedlings. PARG1 and PARG2 play an essential and a minor role, respectively under the same conditions. Mutation of PARG1 results in increased DNA damage level and enhanced cell death in plants after bleomycin treatment.PARG1expression is induced primarily in root and shoot meristems by bleomycin and induction ofPARG1is dependent on ATM and ATR kinases. PARG1 also antagonistically modulates the DNA repair process by preventing the over-induction of DNA repair genes. Our study determined the contribution of each PARP and PARG member in DNA repair and indicated that PARG1 plays a critical role in this process.
Systemic differences in serum metabolome: a cross sectional comparison of women with localised and widespread pain and controls
Authors: Hadrévi J. , Björklund M. , Kosek E. , Hällgren S. , Antti H. , Fahlström M. , Hellström F. 
Published: November 2015

AbstractChronic musculoskeletal pain exists either as localised to a single region or as widespread to multiple sites in several quadrants of the body. Prospective studies indicate that widespread pain could act as a far end of a continuum of musculoskeletal pain that started with chronic localised pain. The mechanism by which the transition from localised pain to widespread occurs is not clear, although many studies suggest it to be an altered metabolism. In this study, systemic metabolic differences between women with chronic localised neck-shoulder pain (NP), women with chronic widespread pain (CWP) and women who were healthy (CON) were assessed. Blood samples were analysed taking a metabolomics approach using gas chromatography mass spectrometry (GC-MS) and orthogonal partial least square discriminant analysis (OPLS-DA). The metabolomics analysis showed a clear systematic difference in the metabolic profiles between the subjects with NP and the CON but only a weak systematic difference between the subjects with CWP and the CON. This most likely reflects a difference in the portion of the metabolome influenced by the two pain conditions. In the NP group, the overall metabolic profile suggests that processes related to energy utilisation and lipid metabolism could be central aspects of mechanisms maintaining disorder.
Dual Tuning of Biomass-Derived Hierarchical Carbon Nanostructures for Supercapacitors: the Role of Balanced Meso/Microporosity and Graphene
Authors: Zhu Zhengju , Jiang Hao , Guo Shaojun , Cheng Qilin , Hu Yanjie , Li Chunzhong 
Published: October 2015

AbstractRational design of advanced carbon nanomaterials with a balanced mesoporosity to microporosity is highly desirable for achieving high energy/power density for supercapacitors because the mesopore can allow better transport pathways for the solvated ions of larger than 1 nm. Inspired by the inherent meso/macroporous architecture and huge absorption ability to aqueous solution of auricularia biomass, we demonstrate a new biomass-derived synthesis process for the three-dimensional (3D) few-layered graphene nanosheets incorporated hierarchical porous carbon (GHPC) nanohybrids. The as-prepared GHPC nanohybrids possess a balanced mesoporosity to microporosity with much improved conductivity, which is highly desirable for achieving high energy/power density for supercapacitors. As we predicted, they delivered a high specific capacitance of 256 F g−1 at 1 A g−1 with excellent rate capability (120 F g−1 at 50 A g−1) and long cycle life (92% capacity retention after 10000 cycles) for symmetric supercapacitors in 1 M H2SO4. Based on the as-obtained carbon materials, a flexible and all-solid-state supercapacitor was also assembled, which can be fully recharged within 10 s and able to light an LED even under bended state. Such excellent performance is at least comparable to the best reports in the literature for two-electrode configuration under aqueous systems.
Structural phase transitions in Bi2Se3 under high pressure
Authors: Yu Zhenhai , Wang Lin , Hu Qingyang , Zhao Jinggeng , Yan Shuai , Yang Ke , Sinogeikin Stanislav , Gu Genda , Mao Ho-kwang 
Published: November 2015

AbstractRaman spectroscopy and angle dispersive X-ray diffraction (XRD) experiments of bismuth selenide (Bi2Se3) have been carried out to pressures of 35.6 and 81.2 GPa, respectively, to explore its pressure-induced phase transformation. The experiments indicate that a progressive structural evolution occurs from an ambient rhombohedra phase (Space group (SG): R-3m) to monoclinic phase (SG: C2/m) and eventually to a high pressure body-centered tetragonal phase (SG: I4/mmm). Evidenced by our XRD data up to 81.2 GPa, the Bi2Se3 crystallizes into body-centered tetragonal structures rather than the recently reported disordered body-centered cubic (BCC) phase. Furthermore, first principles theoretical calculations favor the viewpoint that the I4/mmm phase Bi2Se3 can be stabilized under high pressure (>30 GPa). Remarkably, the Raman spectra of Bi2Se3 from this work (two independent runs) are still Raman active up to ~35 GPa. It is worthy to note that the disordered BCC phase at 27.8 GPa is not observed here. The remarkable difference in atomic radii of Bi and Se in Bi2Se3 may explain why Bi2Se3 shows different structural behavior than isocompounds Bi2Te3 and Sb2Te3.
Screen printed passive components for flexible power electronics
Authors: Ostfeld Aminy E. , Deckman Igal , Gaikwad Abhinav M. , Lochner Claire M. , Arias Ana C. 
Published: October 2015

AbstractAdditive and low-temperature printing processes enable the integration of diverse electronic devices, both power-supplying and power-consuming, on flexible substrates at low cost. Production of a complete electronic system from these devices, however, often requires power electronics to convert between the various operating voltages of the devices. Passive components—inductors, capacitors and resistors—perform functions such as filtering, short-term energy storage and voltage measurement, which are vital in power electronics and many other applications. In this paper, we present screen-printed inductors, capacitors, resistors and an RLC circuit on flexible plastic substrates and report on the design process for minimization of inductor series resistance that enables their use in power electronics. Printed inductors and resistors are then incorporated into a step-up voltage regulator circuit. Organic light-emitting diodes and a flexible lithium ion battery are fabricated and the voltage regulator is used to power the diodes from the battery, demonstrating the potential of printed passive components to replace conventional surface-mount components in a DC-DC converter application.
The importance of eukaryotic ferritins in iron handling and cytoprotection
Authors: Arosio Paolo , Carmona Fernando , Gozzelino Raffaella , Maccarinelli Federica , Poli Maura 
Published: October 2015

Ferritins, the main intracellular iron storage proteins, have been studied for over 60 years, mainly focusing on the mammalian ones. This allowed the elucidation of the structure of these proteins and the mechanisms regulating their iron incorporation and mineralization. However, ferritin is present in most, although not all, eukaryotic cells, comprising monocellular and multicellular invertebrates and vertebrates. The aim of this review is to provide an update on the general properties of ferritins that are common to various eukaryotic phyla (except plants), and to give an overview on the structure, function and regulation of ferritins. An update on the animal models that were used to characterize H, L and mitochondrial ferritins is also provided. The data show that ferritin structure is highly conserved among different phyla. It exerts an important cytoprotective function against oxidative damage and plays a role in innate immunity, where it also contributes to prevent parenchymal tissue from the cytotoxicity of pro-inflammatory agonists released by the activation of the immune response activation. Less clear are the properties of the secretory ferritins expressed by insects and molluscs, which may be important for understanding the role played by serum ferritin in mammals.
The Unplanned Postoperative Coronary Angiogram after CABG: Identifying the Patients at Risk
Authors: Issam Ismail , Martens Andreas , Cebotari Serghei , Haverich Axel , Shrestha Malakh , Fleißner Felix 
Published: October 2015

Objectives Coronary artery bypass grafting (CABG) is the “gold standard” for patients with multiple vessel coronary artery disease (CAD). However, there is no “gold standard” to control bypass patency immediately postoperatively. “Post-completion” control angiogram (CA) is not routinely performed. We retrospectively analyzed the data of all patients undergoing urgent coronary angiogram post-CABG at our center.
Methods Between January 2005 and June 2011, a total of 6,025 patients underwent CABG (isolated or combined) for CAD in our hospital. In patients who underwent urgent postoperative CA, high serum cardiac enzymes (>100 CK-MB), severe new ECG changes, or unexpected low left ventricular function were present.
Results A total of 106 patients (1.8%) underwent post-CABG urgent coronary angiogram. Overall 30-day mortality in this cohort was 8.5%. The average time between the cardiac operation and the coronary angiogram in these patients was 3.41 ± 5.68 days. The rates for an urgent coronary angiogram were 1.3% (n = 25), 2% (n = 65), and 1.8% (n = 16) for total arterial, combined arterial, and venous and solely venous CABG, respectively. Twenty-four percent of patients underwent CABG bypass revision, while 32% of the patients underwent PTCA, stenting, or both. Younger patients, female patients, smaller patients, and patients receiving a combined arterial and venous revascularization were at a higher risk for an unplanned postoperative CA in the multivariate risk analysis.
Conclusion This study shows that the necessity for urgent post-CABG coronary angiogram is low (1.8%). However, more than half of the patients undergoing postoperative coronary angiogram needed reintervention, and, in spite of it, had high mortality. “Completion” control angiogram is not always feasible, patients at higher risk (e.g., female patients) should be identified and post-CABG coronary angiogram performed as soon as possible without undue delay, or a primary hybrid approach with an intraoperative CA should be applied.
Protael: protein data visualization library for the web
Authors: Sedova Mayya , Jaroszewski Lukasz , Godzik Adam 
Published: October 2015

Abstract
Summary: Protael is a JavaScript library for creating interactive visualizations of biological sequences and various associated data. It allows users to generate high-quality vector graphics (SVG) and integrate it into web pages.
Availability and implementation: Protael distribution, documentation and examples are freely available at http://protael.org; source code is hosted at https://github.com/sanshu/protaeljs.
Contact: adam@godziklab.org
SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence
Authors: Yao Po-Ju , Chung Ren-Hua 
Published: October 2015

Abstract
Summary: It is difficult for current simulation tools to simulate sequence data in a pre-specified pedigree structure and pre-specified affection status. Previously, we developed a flexible tool, SeqSIMLA2, for simulating sequence data in either unrelated case-control or family samples with different disease and quantitative trait models. Here we extended the tool to efficiently simulate sequences with multiple disease sites in large pedigrees with a given disease status for each pedigree member, assuming that the disease prevalence is low.
Availability and implementation: SeqSIMLA2_exact is implemented with C++ and is available at http://seqsimla.sourceforge.net.
Contact: rchung@nhri.org.tw
TB or Not TB
Authors: Guo Ming , Mak Susanna , Reiss Dina , Salit Irving E. , Ouzounian Maral 
Published: October 2015

Abstract

Bartonella quintana infection is commonly associated with alcohol abuse and homelessness and can be a cause of blood culture-negative infective endocarditis. Bartonella endocarditis has a subacute clinical course and can cause severe valvular disruption with potentially fatal outcomes. Its diagnosis requires a high index of suspicion in the clinical scenario of culture-negative endocarditis and may require serological testing, western blotting, or culture in specialized media. 16S RNA amplification sequencing analysis and histopathological examination may be helpful if a surgical specimen is available. We present a case of blood culture-negative infective endocarditis in the context of active pulmonary tuberculosis; endocarditis caused by Mycobacteria tuberculosis is extremely rare so another cause of the endocarditis was sought. Bartonella quintana was confirmed as the cause by molecular detection done on the vegetation.
Resonant leaders: an impetus to change the organizations
Authors: Chawla Saniya , Lenka Usha 
Published: October 2015

Purpose
– The purpose of the paper is to discuss about being a resonant leader during a change process of learning, unlearning and relearning.

Design/methodology/approach
– The paper is a viewpoint.

Findings
– To embrace and accept change in the organization, emotionally intelligent resonant leaders are required who would guide them through shared vision, compassion and overall positive moods.

Originality/value
– The paper makes a pioneering effort to explain new type of leadership style necessary for any change to occur in the organizations.