bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective flow-induced vesicle rupture to sort by membrane mechanical properties
Authors: Pommella Angelo , Brooks Nicholas J. , Seddon John M. , Garbin Valeria 
Published: August 2015

AbstractVesicle and cell rupture caused by large viscous stresses in ultrasonication is central to biomedical and bioprocessing applications. The flow-induced opening of lipid membranes can be exploited to deliver drugs into cells, or to recover products from cells, provided that it can be obtained in a controlled fashion. Here we demonstrate that differences in lipid membrane and vesicle properties can enable selective flow-induced vesicle break-up. We obtained vesicle populations with different membrane properties by using different lipids (SOPC, DOPC, or POPC) and lipid:cholesterol mixtures (SOPC:chol and DOPC:chol). We subjected vesicles to large deformations in the acoustic microstreaming flow generated by ultrasound-driven microbubbles. By simultaneously deforming vesicles with different properties in the same flow, we determined the conditions in which rupture is selective with respect to the membrane stretching elasticity. We also investigated the effect of vesicle radius and excess area on the threshold for rupture and identified conditions for robust selectivity based solely on the mechanical properties of the membrane. Our work should enable new sorting mechanisms based on the difference in membrane composition and mechanical properties between different vesicles, capsules, or cells.
Comparison of four digital PCR platforms for accurate quantification of DNA copy number of a certified plasmid DNA reference material
Authors: Dong Lianhua , Meng Ying , Sui Zhiwei , Wang Jing , Wu Liqing , Fu Boqiang 
Published: August 2015

AbstractDigital polymerase chain reaction (dPCR) is a unique approach to measurement of the absolute copy number of target DNA without using external standards. However, the comparability of different dPCR platforms with respect to measurement of DNA copy number must be addressed before dPCR can be classified fundamentally as an absolute quantification technique. The comparability of four dPCR platforms with respect to accuracy and measurement uncertainty was investigated by using a certified plasmid reference material. Plasmid conformation was found to have a significant effect on droplet-based dPCR (QX100 and RainDrop) not shared with chip-based QuantStudio 12k or BioMark. The relative uncertainty of partition volume was determined to be 0.7%, 0.8%, 2.3% and 2.9% for BioMark, QX100, QuantStudio 12k and RainDrop, respectively. The measurements of the certified pNIM-001 plasmid made using the four dPCR platforms were corrected for partition volume and closely consistent with the certified value within the expended uncertainty. This demonstrated that the four dPCR platforms are of comparable effectiveness in quantifying DNA copy number. These findings provide an independent assessment of this method of determining DNA copy number when using different dPCR platforms and underline important factors that should be taken into consideration in the design of dPCR experiments.
Edge states and integer quantum Hall effect in topological insulator thin films
Authors: Zhang Song-Bo , Lu Hai-Zhou , Shen Shun-Qing 
Published: August 2015

AbstractThe integer quantum Hall effect is a topological state of quantum matter in two dimensions and has recently been observed in three-dimensional topological insulator thin films. Here we study the Landau levels and edge states of surface Dirac fermions in topological insulators under strong magnetic field. We examine the formation of the quantum plateaux of the Hall conductance and find two different patterns, in one pattern the filling number covers all integers while only odd integers in the other. We focus on the quantum plateau closest to zero energy and demonstrate the breakdown of the quantum spin Hall effect resulting from structure inversion asymmetry. The phase diagrams of the quantum Hall states are presented as functions of magnetic field, gate voltage and chemical potential. This work establishes an intuitive picture of the edge states to understand the integer quantum Hall effect for Dirac electrons in topological insulator thin films.
Control of Dzyaloshinskii-Moriya interaction in Mn1−xFexGe: a first-principles study
Authors: Koretsune Takashi , Nagaosa Naoto , Arita Ryotaro 
Published: August 2015

AbstractMotivated by the recent experiment on the size and helicity control of skyrmions in Mn1−xFexGe, we study how the Dzyaloshinskii-Moriya (DM) interaction changes its size and sign in metallic helimagnets. By means of first-principles calculations, we successfully reproduce the non-trivial sign change of the DM interaction observed in the experiment. While the DM interaction sensitively depends on the carrier density or the detail of the electronic structure such as the size of the exchange splitting, its behavior can be systematically understood in terms of the distribution of anticrossing points in the band structure. By following this guiding principle, we can even induce gigantic anisotropy in the DM interaction by applying a strain to the system. These results pave the new way for skyrmion crystal engineering in metallic helimagnets.
Hsa-miR-19a is associated with lymph metastasis and mediates the TNF-α induced epithelial-to-mesenchymal transition in colorectal cancer
Authors: Huang Lanlan , Wang Xiaoyan , Wen Chuangyu , Yang Xiangling , Song Minmin , Chen Junxiong , Wang Chenliang , Zhang Bo , Wang Lei , Iwamoto Aikichi , Wang Jianping , Liu Huanliang 
Published: August 2015

AbstractLymph node metastasis is an important factor determining the outcome of colorectal cancer. Although epithelial-to-mesenchymal transition (EMT), TNF-α and microRNA (miRNA) have been found to play important roles in lymph node metastasis, the underlying molecular mechanism remains unclear. Here we reported that high expression of microRNA-19a (miR-19a) was associated with lymph node metastasis and played an important role in TNF-α-induced EMT in colorectal cancer (CRC) cells. We analyzed miR-19a expression in surgical tissue specimens from 11 CRC patients and 275 formalin-fixed, paraffin-embedded CRC patients. We found that miR-19a was up-regulated in CRC tissues and high expression of miR-19a was significantly associated with lymph node metastasis. We further analyzed miR-19a lymph node metastasis signature in an external validation cohort of 311 CRC cases of the TCGA. MiR-19a was found to be significantly associated with lymph node metastasis in rectal cancer. In vitro, we showed that overexpression of miR-19a in human CRC cell lines promoted cell invasion and EMT. Furthermore, miR-19a was up-regulated by TNF-α and miR-19a was required for TNF-α-induced EMT and metastasis in CRC cells. Collectively, miR-19a played an important role in mediating EMT and metastatic behavior in CRC. It may serve as a potential marker of lymph node metastasis.
Integrated Transcriptomics Establish Macrophage Polarization Signatures and have Potential Applications for Clinical Health and Disease
Authors: Becker Matheus , De Bastiani Marco A. , Parisi Mariana M. , Guma Fátima T. C. R. , Markoski Melissa M. , Castro Mauro A. A. , Kaplan Mark H. , Barbé-Tuana Florencia M. , Klamt Fábio 
Published: August 2015

AbstractGrowing evidence defines macrophages (Mφ) as plastic cells with wide-ranging states of activation and expression of different markers that are time and location dependent. Distinct from the simple M1/M2 dichotomy initially proposed, extensive diversity of macrophage phenotypes have been extensively demonstrated as characteristic features of monocyte-macrophage differentiation, highlighting the difficulty of defining complex profiles by a limited number of genes. Since the description of macrophage activation is currently contentious and confusing, the generation of a simple and reliable framework to categorize major Mφ phenotypes in the context of complex clinical conditions would be extremely relevant to unravel different roles played by these cells in pathophysiological scenarios. In the current study, we integrated transcriptome data using bioinformatics tools to generate two macrophage molecular signatures. We validated our signatures in in vitro experiments and in clinical samples. More importantly, we were able to attribute prognostic and predictive values to components of our signatures. Our study provides a framework to guide the interrogation of macrophage phenotypes in the context of health and disease. The approach described here could be used to propose new biomarkers for diagnosis in diverse clinical settings including dengue infections, asthma and sepsis resolution.
Non-Markovian Complexity in the Quantum-to-Classical Transition
Authors: Xiong Heng-Na , Lo Ping-Yuan , Zhang Wei-Min , Feng Da Hsuan , Nori Franco 
Published: August 2015

AbstractThe quantum-to-classical transition is due to environment-induced decoherence and it depicts how classical dynamics emerges from quantum systems. Previously, the quantum-to-classical transition has mainly been described with memory-less (Markovian) quantum processes. Here we study the complexity of the quantum-to-classical transition through general non-Markovian memory processes. That is, the influence of various reservoirs results in a given initial quantum state evolving into one of the following four scenarios: thermal state, thermal-like state, quantum steady state, or oscillating quantum nonstationary state. In the latter two scenarios, the system maintains partial or full quantum coherence due to the strong non-Markovian memory effect, so that in these cases, the quantum-to-classical transition never occurs. This unexpected new feature provides a new avenue for the development of future quantum technologies because the remaining quantum oscillations in steady states are decoherence-free.
Cordycepin induced MA-10 mouse Leydig tumor cell apoptosis by regulating p38 MAPKs and PI3K/AKT signaling pathways
Authors: Pan Bo-Syong , Wang Yang-Kao , Lai Meng-Shao , Mu Yi-Fen , Huang Bu-Miin 
Published: August 2015

AbstractThe p38 MAPKs play important roles in the regulation of balance between cell survival and cell death on the development of various cancers. However, the roles of p38 MAPKs regulating apoptotic effects on Leydig tumor cells remain unclear. In the present study, we showed that cordycepin (3′-deoxyadenosine) selectively induced apoptosis in MA-10 mouse Leydig tumor cells through regulating the p38 MAPK and PI3K/AKT signaling pathways. Cordycepin reduced viability in MA-10, TM4 and NT2/D1 cells, but not cause cell death of primary mouse Leydig cells on moderate concentration. Cordycepin increased reactive oxygen species (ROS) levels, which is associated with the induction of apoptosis as characterized by positive Annexin V binding, activation of caspase-3 and cleavage of PARP. Inhibition of p38 MAPKs activity by SB203580 significantly prevented cordycepin-induced apoptosis in MA-10 cells. Co-treatment with wortmannin or the autophagy inhibitor 3-methyladenine (3-MA) elevated levels of apoptosis in cordycepin-treated MA-10 cells. Moreover, cordycepin activated p53, p21 and TGFß; and downregulated CDK2. The antitumour activity of cordycepin-treated MA-10 cells was significantly distinct in severe combined immunodeficiency (SCID) micein vivo. These results suggested that cordycein is a highly selective treatment to induce MA-10 cells apoptosis via p38 MAPKs signaling.
Selective enrichment of mycobacterial proteins from infected host macrophages
Authors: Chande Ajit G. , Siddiqui Zaved , Midha Mukul Kumar , Sirohi Varsha , Ravichandran Srikanth , Rao Kanury V. S. 
Published: August 2015

AbstractUpon infection, Mycobacterium tuberculosis (Mtb) deploys specialized secretion machinery to deliver virulent proteins with the capacity to modulate a variety of host-cellular pathways. Studies on the identification of intra-macrophage Mtb proteins, however, are constricted by an inability to selectively enrich these virulent effectors against overwhelming protein content of the host. Here, we introduce an Mtb-selective protein labeling method based on genetic incorporation of azidonorleucine (Anl) through the expression of a mutant methionyl-tRNA synthetase. Exclusive incorporation of Anl, into native Mtb proteins, provided a click handle to pull out low abundant secretory proteins from the lysates of infected cells. Further, temporal secretome profiling, upon infection with strains of varying degree of virulence, revealed the proficiency of virulent Mtb to secrete chaperones. This ability contributed at least partially to the mycobacterial virulence-specific suppression of ER stress in the host macrophage, representing an important facet of mycobacterial virulence. The Anl labeling approach should facilitate new exciting opportunities for imaging and proteomic investigations of differently virulent Mtb isolates to understand determinants of pathogenicity.
Mass Spectrometry-based PhyloProteomics (MSPP): A novel microbial typing Method
Authors: Zautner Andreas Erich , Masanta Wycliffe Omurwa , Weig Michael , Groß Uwe , Bader Oliver 
Published: August 2015

AbstractMALDI-TOF-MS of microorganisms, which identifies microbes based on masses of high abundant low molecular weight proteins, is rapidly advancing to become another standard method in clinical routine laboratory diagnostics. Allelic isoforms of these proteins result in varying masses of detectable biomarker ions. These variations give rise to a novel typing method for microorganisms named mass spectrometry-based phyloproteomics (MSPP). The base of MSPP is an amino acid sequence list of allelic isoforms caused by non-synonymous mutations in biomarker genes, which were detectable as mass shifts in an overlay of calibrated MALDI-TOF spectra. Thus, for each isolate a combination of amino acid sequences can be deduced from the scheme of recordable biomarker masses. Performing comparably to laborious multilocus and whole genome sequence typing (wgMLST)-approaches it is feasible to build phyloproteomic dendrograms using hierarchical cluster analysis. MSPP bears a high potential especially for identification of chromosomal localised virulence or antimicrobial resistance factors associated with evolutionary relatedness. In this study the principle of MSPP-typing was demonstrated on a Campylobacter jejuni ssp. jejuni isolate collection and MSPP was compared to MLST.
Bi-crystallographic lattice structure directs grain boundary motion under shear stress
Authors: Wan Liang , Han Weizhong , Chen Kai 
Published: August 2015

AbstractShear stress driven grain boundary (GB) migration was found to be a ubiquitous phenomenon in small grained polycrystalline materials. Here we show that the GB displacement shift complete (DSC) dislocation mechanism for GB shear coupled migration is still functioning even if the geometry orientation of the GBs deviates a few degrees from the appropriate coincidence site lattice (CSL) GBs. It means that any large angle GB can have a considerable chance to be such a “CSL-related GB” for which the shear coupled GB migration motion can happen by the GB DSC dislocation mechanism. We conclude that the CSL-DSC bi-crystallographic lattice structure in GB is the main reason that GB can migrate under shear stress.
Efficacy of progesterone for moderate to severe traumatic brain injury: a meta-analysis of randomized clinical trials
Authors: Lin Chao , He Hongquan , Li Zheng , Liu Yinglong , Chao Honglu , Ji Jing , Liu Ning 
Published: August 2015

AbstractProgesterone has been shown to have neuroprotective effects in multiple animal models of brain injury, whereas the efficacy and safety in patients with traumatic brain injury (TBI) remains contentious. Here, a total of seven randomized controlled trials (RCTs) with 2492 participants were included to perform this meta-analysis. Compared with placebo, there was no significant decrease to be found in the rate of death or vegetative state for patients with acute TBI (RR = 0.88, 95%CI = 0.70, 1.09, p = 0.24). Furthermore, progesterone was not associated with good recovery in comparison with placebo (RR = 1.00, 95%CI = 0.88, 1.14, p = 0.95). Together, our study suggested that progesterone did not improve outcomes over placebo in the treatment of acute TBI.
CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data
Authors: Kumar Praveen Kumar Raj , Hoang Thanh V. , Robinson Michael L. , Tsonis Panagiotis A. , Liang Chun 
Published: August 2015

AbstractThe fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for downstream analysis. To facilitate this choice, we designed a novel tool for comparing alignment results of user data based on the relative reliability of uniquely aligned reads (CADBURE). CADBURE can easily evaluate different aligners, or different parameter sets using the same aligner and selects the best alignment result for any RNA-Seq dataset. Strengths of CADBURE include the ability to compare alignment results without the need for synthetic data such as simulated genomes, alignment regeneration and randomly subsampled datasets. The benefit of a CADBURE selected alignment result was supported by differentially expressed gene (DEG) analysis. We demonstrated that the use of CADBURE to select the best alignment from a number of different alignment results could change the number of DEGs by as much as 10%. In particular, the CADBURE selected alignment result favors fewer false positives in the DEG analysis. We also verified differential expression of eighteen genes with RT-qPCR validation experiments. CADBURE is an open source tool (http://cadbure.sourceforge.net/).
Tailoring phase slip events through magnetic doping in superconductor-ferromagnet composite films
Authors: Bawa Ambika , Jha Rajveer , Sahoo Sangeeta 
Published: August 2015

AbstractThe interplay between superconductivity (SC) and ferromagnetism (FM) when embedded together has attracted unprecedented research interest due to very rare coexistence of these two phenomena. The focus has been mainly put into the proximity induced effects like, coexistence of magnetism and superconductivity, higher critical current, triplet superconductivity etc. However, very little attention has been paid experimentally to the role of magnetic constituent on triggering phase slip processes in the composite films (CFs). We demonstrate that less than 1 at.% of magnetic contribution in the CFs can initiate phase slip events efficiently. Due to advanced state-of-the-art fabrication techniques, phase slip based studies have been concentrated mainly on superconducting nanostructures. Here, we employ wide mesoscopic NbGd based CFs to study the phase slip processes. Low temperature current-voltage characteristics (IVCs) of CFs show stair-like features originated through phase slip events and are absent in pure SC films. Depending on the bias current and temperature, distinct regions, dominated by Abrikosov type vortex-antivortex (v-av) pairs and phase slip events, are observed. The results presented here open a new way to study the phase slip mechanism, its interaction with v-av pairs in two dimensions and hence can be useful for future photonic and metrological applications.
Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems
Authors: Long Wenmin , Xue Zhengsheng , Zhang Qianpeng , Feng Zhou , Bridgewater Laura , Wang Linghua , Zhao Liping , Pang Xiaoyan 
Published: August 2015

AbstractThe same prebiotics have produced inconsistent effects on microbiota when evaluated in different batch fermentation studies. To understand the reasons behind these discrepancies, we compared impact of one prebiotic formula on the same inoculated fecal microbiota in two frequently used batch systems: phosphate-buffered saline (PBS, oligotrophic) and basal culture medium (BCM, eutrophic). The microbiota was monitored using 454 pyrosequencing. Negative controls (no prebiotic) of both systems showed significant shifts in the microbiota during fermentation, although their pH remained relatively stable, especially in BCM, with increases in Bilophila and Escherichia/Shigella but a decrease in Faecalibacterium. We identified prebiotic responders via redundancy analysis by including both baseline and negative controls. The key positive and negative responders in the two systems were very different, with only 8 consistently modulated OTUs (7 of the 28 positive responders and 1 of the 35 negative responders). Moreover, some OTUs within the same genus responded to the prebiotic in opposite ways. Therefore, to obtain a complete in vitro evaluation of the modulatory effects of a prebiotic on microbiota, it is necessary to use both oligotrophic and eutrophic systems, compare treatment groups with both baseline and negative controls and analyze the microbiota changes down to the OTU level.
Neural networks underlying implicit and explicit moral evaluations in psychopathy
Authors: Yoder K J , Harenski C , Kiehl K A , Decety J 
Published: August 2015

AbstractPsychopathy, characterized by symptoms of emotional detachment, reduced guilt and empathy and a callous disregard for the rights and welfare of others, is a strong risk factor for immoral behavior. Psychopathy is also marked by abnormal attention with downstream consequences on emotional processing. To examine the influence of task demands on moral evaluation in psychopathy, functional magnetic resonance imaging was used to measure neural response and functional connectivity in 88 incarcerated male subjects (28 with Psychopathy Checklist Revised (PCL-R) scores ⩾30) while they viewed dynamic visual stimuli depicting interpersonal harm and interpersonal assistance in two contexts, implicit and explicit. During the implicit task, high psychopathy was associated with reduced activity in the dorsolateral prefrontal cortex and caudate when viewing harmful compared with helpful social interactions. Functional connectivity seeded in the right amygdala and right temporoparietal junction revealed decreased coupling with the anterior cingulate cortex (ACC), anterior insula, striatum and ventromedial prefrontal cortex. In the explicit task, higher trait psychopathy predicted reduced signal change in ACC and amygdala, accompanied by decreased functional connectivity to temporal pole, insula and striatum, but increased connectivity with dorsal ACC. Psychopathy did not influence behavioral performance in either task, despite differences in neural activity and functional connectivity. These findings provide the first direct evidence that hemodynamic activity and neural coupling within the salience network are disrupted in psychopathy, and that the effects of psychopathy on moral evaluation are influenced by attentional demands.