bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying microstructural dynamics and electrochemical activity of graphite and silicon-graphite lithium ion battery anodes
Authors: Pietsch Patrick , Westhoff Daniel , Feinauer Julian , Eller Jens , Marone Federica , Stampanoni Marco , Schmidt Volker , Wood Vanessa 
Published: September 2016

AbstractDespite numerous studies presenting advances in tomographic imaging and analysis of lithium ion batteries, graphite-based anodes have received little attention. Weak X-ray attenuation of graphite and, as a result, poor contrast between graphite and the other carbon-based components in an electrode pore space renders data analysis challenging. Here we demonstrate operando tomography of weakly attenuating electrodes during electrochemical (de)lithiation. We use propagation-based phase contrast tomography to facilitate the differentiation between weakly attenuating materials and apply digital volume correlation to capture the dynamics of the electrodes during operation. After validating that we can quantify the local electrochemical activity and microstructural changes throughout graphite electrodes, we apply our technique to graphite-silicon composite electrodes. We show that microstructural changes that occur during (de)lithiation of a pure graphite electrode are of the same order of magnitude as spatial inhomogeneities within it, while strain in composite electrodes is locally pronounced and introduces significant microstructural changes.
Tissue engineering of acellular vascular grafts capable of somatic growth in young lambs
Authors: Syedain Zeeshan , Reimer Jay , Lahti Matthew , Berry James , Johnson Sandra , Bianco Richard , Tranquillo Robert T. 
Published: September 2016

AbstractTreatment of congenital heart defects in children requiring right ventricular outflow tract reconstruction typically involves multiple open-heart surgeries because all existing graft materials have no growth potential. Here we present an ‘off-the-shelf’ vascular graft grown from donor fibroblasts in a fibrin gel to address this critical unmet need. In a proof-of-concept study, the decellularized grafts are implanted as a pulmonary artery replacement in three young lambs and evaluated to adulthood. Longitudinal ultrasounds document dimensional growth of the grafts. The lambs show normal growth, increasing body weight by 366% and graft diameter and volume by 56% and 216%, respectively. Explanted grafts display physiological strength and stiffness, complete lumen endothelialization and extensive population by mature smooth muscle cells. The grafts also show substantial elastin deposition and a 465% increase in collagen content, without signs of calcification, aneurysm or stenosis. Collectively, our data support somatic growth of this completely biological graft.
The mechanism of eutectic growth in highly anisotropic materials
Authors: Shahani Ashwin J. , Xiao Xianghui , Voorhees Peter W. 
Published: September 2016

AbstractIn the past 50 years, there has been increasing interest—both theoretically and experimentally—in the problem of pattern formation of a moving boundary, such as a solidification front. One example of pattern formation is that of irregular eutectic solidification, in which the solid–liquid interface is non-isothermal and the interphase spacing varies in ways that are poorly understood. Here, we identify the growth mode of irregular eutectics, using reconstructions from four-dimensional (that is, time and space resolved) X-ray microtomography. Our results show that the eutectic growth process can be markedly different from that seen in previously used model systems and theories based on the ex situ analysis of microstructure. In light of our experimental findings, we present a coherent growth model of irregular eutectic solidification.
Observation of a new superfluid phase for 3He embedded in nematically ordered aerogel
Authors: Zhelev N. , Reichl M. , Abhilash T. S. , Smith E. N. , Nguyen K. X. , Mueller E. J. , Parpia J. M. 
Published: September 2016

AbstractIn bulk superfluid 3He at zero magnetic field, two phases emerge with the B-phase stable everywhere except at high pressures and temperatures, where the A-phase is favoured. Aerogels with nanostructure smaller than the superfluid coherence length are the only means to introduce disorder into the superfluid. Here we use a torsion pendulum to study 3He confined in an extremely anisotropic, nematically ordered aerogel consisting of ∼10 nm-thick alumina strands, spaced by ∼100 nm, and aligned parallel to the pendulum axis. Kinks in the development of the superfluid fraction (at various pressures) as the temperature is varied correspond to phase transitions. Two such transitions are seen in the superfluid state, and we identify the superfluid phase closest to Tc at low pressure as the polar state, a phase that is not seen in bulk 3He.
Alterations in the hippocampus and thalamus in individuals at high risk for psychosis
Authors: Harrisberger Fabienne , Buechler Roman , Smieskova Renata , Lenz Claudia , Walter Anna , Egloff Laura , Bendfeldt Kerstin , Simon Andor E , Wotruba Diana , Theodoridou Anastasia , Rössler Wulf , Riecher-Rössler Anita , Lang Undine E , Heekeren Karsten , Borgwardt Stefan 
Published: September 2016

AbstractReduction in hippocampal volume is a hallmark of schizophrenia and already present in the clinical high-risk state. Nevertheless, other subcortical structures, such as the thalamus, amygdala and pallidum can differentiate schizophrenia patients from controls. We studied the role of hippocampal and subcortical structures in clinical high-risk individuals from two cohorts. High-resolution T1-weighted structural MRI brain scans of a total of 91 clinical high-risk individuals and 64 healthy controls were collected in two centers. The bilateral volume of the hippocampus, the thalamus, the caudate, the putamen, the pallidum, the amygdala, and the accumbens were automatically segmented using FSL-FIRST. A linear mixed-effects model and a prospective meta-analysis were applied to assess group-related volumetric differences. We report reduced hippocampal and thalamic volumes in clinical high-risk individuals compared to healthy controls. No volumetric alterations were detected for the caudate, the putamen, the pallidum, the amygdala, or the accumbens. Moreover, we found comparable medium effect sizes for group-related comparison of the thalamus in the two analytical methods. These findings underline the relevance of specific alterations in the hippocampal and subcortical volumes in the high-risk state. Further analyses may allow hippocampal and thalamic volumes to be used as biomarkers to predict psychosis.
Switching from weakly to strongly limited injection in self-aligned, nano-patterned organic transistors
Authors: Zojer Karin , Rothländer Thomas , Kraxner Johanna , Schmied Roland , Palfinger Ursula , Plank Harald , Grogger Werner , Haase Anja , Gold Herbert , Stadlober Barbara 
Published: September 2016

AbstractOrganic thin-film transistors for high frequency applications require large transconductances in combination with minimal parasitic capacitances. Techniques aiming at eliminating parasitic capacitances are prone to produce a mismatch between electrodes, in particular gaps between the gate and the interlayer electrodes. While such mismatches are typically undesirable, we demonstrate that, in fact, device structures with a small single-sided interlayer electrode gap directly probe the detrimental contact resistance arising from the presence of an injection barrier. By employing a self-alignment nanoimprint lithography technique, asymmetric coplanar organic transistors with an intentional gap of varying size (< 0.2 μm) between gate and one interlayer electrode are fabricated. An electrode overlap exceeding 1 μm with the other interlayer has been kept. Gaps, be them source or drain-sided, do not preclude transistor operation. The operation of the device with a source-gate gap reveals a current reduction up to two orders of magnitude compared to a source-sided overlap. Drift-diffusion based simulations reveal that this marked reduction is a consequence of a weakened gate-induced field at the contact which strongly inhibits injection.
DNA methylation profile of triple negative breast cancer-specific genes comparing lymph node positive patients to lymph node negative patients
Authors: Mathe Andrea , Wong-Brown Michelle , Locke Warwick J. , Stirzaker Clare , Braye Stephen G. , Forbes John F. , Clark Susan J. , Avery-Kiejda Kelly A. , Scott Rodney J. 
Published: September 2016

AbstractTriple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with no targeted treatment available. Our previous study identified 38 TNBC-specific genes with altered expression comparing tumour to normal samples. This study aimed to establish whether DNA methylation contributed to these expression changes in the same cohort as well as disease progression from primary breast tumour to lymph node metastasis associated with changes in the epigenome. We obtained DNA from 23 primary TNBC samples, 12 matched lymph node metastases, and 11 matched normal adjacent tissues and assayed for differential methylation profiles using Illumina HumanMethylation450 BeadChips. The results were validated in an independent cohort of 70 primary TNBC samples. The expression of 16/38 TNBC-specific genes was associated with alteration in DNA methylation. Novel methylation changes between primary tumours and lymph node metastases, as well as those associated with survival were identified. Altered methylation of 18 genes associated with lymph node metastasis were identified and validated. This study reveals the important role DNA methylation plays in altered gene expression of TNBC-specific genes and lymph node metastases. The novel insights into progression of TNBC to secondary disease may provide potential prognostic indicators for this hard-to-treat breast cancer subtype.
Water uptake mechanism and germination of Erythrina velutina seeds treated with atmospheric plasma
Authors: Alves Junior Clodomiro , de Oliveira Vitoriano Jussier , da Silva Dinnara Layza Souza , de Lima Farias Mikelly , de Lima Dantas Nadjamara Bandeira 
Published: September 2016

AbstractThe effect of plasma applied to mulungu (Erythrina velutina) seeds was studied to verify its influence on the germination, water absorption, wettability and structure of the seeds. The plasma jet used in this study was produced by dielectric barrier discharge (DBD) in a helium gas flow of 0.03 L/s at a distance of 13 mm for 60 s. The plasma treatment significantly affected the seed germination rate, which was approximately 5% higher than that of the untreated group. Micropyle and hilum contributed a greater proportion to uptake. When sealed in the hilar or micropyle regions the amount of water absorbed into the seed decreased approximately 75% compared to the unsealed seed. This difference suggests that these two regions together act cooperatively in the water absorption. However, when plasma treated seed was blocked in the micropyle region, water absorption was higher higher than in seeds blocked hilum. This difference suggests that the plasma treatment changed the wettability of the hilum more effectively than it changed the micropyle. These results indicate that plasma can significantly change the hydrophilicity, water absorption and percentage of seed germination in E. velutina.
Integration and Typologies of Vulnerability to Climate Change: A Case Study from Australian Wheat Sheep Zones
Authors: Huai Jianjun 
Published: September 2016

AbstractAlthough the integrated indicator methods have become popular for assessing vulnerability to climate change, their proliferation has introduced a confusing array of scales and indicators that cause a science-policy gap. I argue for a clear adaptation pathway in an “integrative typology” of regional vulnerability that matches appropriate scales, optimal measurements and adaptive strategies in a six-dimensional and multi-level analysis framework of integration and typology inspired by the “5W1H” questions: “Who is concerned about how to adapt to the vulnerability of what to what in some place (where) at some time (when)?” Using the case of the vulnerability of wheat, barley and oats to drought in Australian wheat sheep zones during 1978–1999, I answer the “5W1H” questions through establishing the “six typologies” framework. I then optimize the measurement of vulnerability through contrasting twelve kinds of vulnerability scores with the divergence of crops yields from their regional mean. Through identifying the socioeconomic constraints, I propose seven generic types of crop-drought vulnerability and local adaptive strategy. Our results illustrate that the process of assessing vulnerability and selecting adaptations can be enhanced using a combination of integration, optimization and typology, which emphasize dynamic transitions and transformations between integration and typology.
Devitalisation of human cartilage by high hydrostatic pressure treatment: Subsequent cultivation of chondrocytes and mesenchymal stem cells on the devitalised tissue
Authors: Hiemer B. , Genz B. , Jonitz-Heincke A. , Pasold J. , Wree A. , Dommerich S. , Bader R. 
Published: September 2016

AbstractThe regeneration of cartilage lesions still represents a major challenge. Cartilage has a tissue-specific architecture, complicating recreation by synthetic biomaterials. A novel approach for reconstruction is the use of devitalised cartilage. Treatment with high hydrostatic pressure (HHP) achieves devitalisation while biomechanical properties are remained. Therefore, in the present study, cartilage was devitalised using HHP treatment and the potential for revitalisation with chondrocytes and mesenchymal stem cells (MSCs) was investigated. The devitalisation of cartilage was performed by application of 480 MPa over 10 minutes. Effective cellular inactivation was demonstrated by the trypan blue exclusion test and DNA quantification. Histology and electron microscopy examinations showed undamaged cartilage structure after HHP treatment. For revitalisation chondrocytes and MSCs were cultured on devitalised cartilage without supplementation of chondrogenic growth factors. Both chondrocytes and MSCs significantly increased expression of cartilage-specific genes. ECM stainings showed neocartilage-like structure with positive AZAN staining as well as collagen type II and aggrecan deposition after three weeks of cultivation. Our results showed that HHP treatment caused devitalisation of cartilage tissue. ECM proteins were not influenced, thus, providing a scaffold for chondrogenic differentiation of MSCs and chondrocytes. Therefore, using HHP-treated tissue might be a promising approach for cartilage repair.
Complex Network Clustering by a Multi-objective Evolutionary Algorithm Based on Decomposition and Membrane Structure
Authors: Ju Ying , Zhang Songming , Ding Ningxiang , Zeng Xiangxiang , Zhang Xingyi 
Published: September 2016

AbstractThe field of complex network clustering is gaining considerable attention in recent years. In this study, a multi-objective evolutionary algorithm based on membranes is proposed to solve the network clustering problem. Population are divided into different membrane structures on average. The evolutionary algorithm is carried out in the membrane structures. The population are eliminated by the vector of membranes. In the proposed method, two evaluation objectives termed as Kernel J-means and Ratio Cut are to be minimized. Extensive experimental studies comparison with state-of-the-art algorithms proves that the proposed algorithm is effective and promising.
Identifying anticancer peptides by using improved hybrid compositions
Authors: Li Feng-Min , Wang Xiao-Qian 
Published: September 2016

AbstractCancer is one of the main causes of threats to human life. Identification of anticancer peptides is important for developing effective anticancer drugs. In this paper, we developed an improved predictor to identify the anticancer peptides. The amino acid composition (AAC), the average chemical shifts (acACS) and the reduced amino acid composition (RAAC) were selected to predict the anticancer peptides by using the support vector machine (SVM). The overall prediction accuracy reaches to 93.61% in jackknife test. The results indicated that the combined parameter was helpful to the prediction for anticancer peptides.
Arachidonic acid mediates the formation of abundant alpha-helical multimers of alpha-synuclein
Authors: Iljina Marija , Tosatto Laura , Choi Minee L. , Sang Jason C. , Ye Yu , Hughes Craig D. , Bryant Clare E. , Gandhi Sonia , Klenerman David 
Published: September 2016

AbstractThe protein alpha-synuclein (αS) self-assembles into toxic beta-sheet aggregates in Parkinson’s disease, while it is proposed that αS forms soluble alpha-helical multimers in healthy neurons. Here, we have made αS multimers in vitro using arachidonic acid (ARA), one of the most abundant fatty acids in the brain, and characterized them by a combination of bulk experiments and single-molecule Fӧrster resonance energy transfer (sm-FRET) measurements. The data suggest that ARA-induced oligomers are alpha-helical, resistant to fibril formation, more prone to disaggregation, enzymatic digestion and degradation by the 26S proteasome, and lead to lower neuronal damage and reduced activation of microglia compared to the oligomers formed in the absence of ARA. These multimers can be formed at physiologically-relevant concentrations, and pathological mutants of αS form less multimers than wild-type αS. Our work provides strong biophysical evidence for the formation of alpha-helical multimers of αS in the presence of a biologically relevant fatty acid, which may have a protective role with respect to the generation of beta-sheet toxic structures during αS fibrillation.
Caloric restriction promotes cell survival in a mouse model of normal tension glaucoma
Authors: Guo Xiaoli , Kimura Atsuko , Azuchi Yuriko , Akiyama Goichi , Noro Takahiko , Harada Chikako , Namekata Kazuhiko , Harada Takayuki 
Published: September 2016

AbstractGlaucoma is characterized by progressive degeneration of retinal ganglion cells (RGCs) and their axons. We previously reported that loss of glutamate transporters (EAAC1 or GLAST) in mice leads to RGC degeneration that is similar to normal tension glaucoma and these animal models are useful in examining potential therapeutic strategies. Caloric restriction has been reported to increase longevity and has potential benefits in injury and disease. Here we investigated the effects of every-other-day fasting (EODF), a form of caloric restriction, on glaucomatous pathology in EAAC1−/−mice. EODF suppressed RGC death and retinal degeneration without altering intraocular pressure. Moreover, visual impairment was ameliorated with EODF, indicating the functional significance of the neuroprotective effect of EODF. Several mechanisms associated with this neuroprotection were explored. We found that EODF upregulated blood β-hydroxybutyrate levels and increased histone acetylation in the retina. Furthermore, it elevated retinal mRNA expression levels of neurotrophic factors and catalase, whereas it decreased oxidative stress levels in the retina. Our findings suggest that EODF, a safe, non-invasive and low-cost treatment, may be available for glaucoma therapy.
Thickness of Actinic Keratosis Does Not Predict Dysplasia Severity or P53 Expression
Authors: Heerfordt Ida M. , Nissen Christoffer V. , Poulsen Thomas , Philipsen Peter A. , Wulf Hans Christian 
Published: September 2016

AbstractThe severity of dysplasia and expression of p53 in actinic keratosis (AK) is of importance for the transformation to squamous cell carcinoma. It is assumed that it is most important to treat thick AKs as they are believed to be more dysplastic than thin AKs. However, a relation between AK thickness and dysplasia or the expression of p53 has never been demonstrated. The aim of this study was to investigate this possible relation. Sixty-six AKs were included for clinical and histological examination. Prior to performing a punch biopsy, the clinical thickness of each AK was measured objectively using two scale bars with a thickness of 0.5 mm and 1 mm. Subsequently, the thickness of the epidermis, the severity of dysplasia and the expression of p53 were assessed histologically. We found a strong and significant positive correlation between measured clinical thickness of the AKs and the histological thickness of epidermis (p < 0.0001). However, the clinical thickness did not correlate with either the severity of dysplasia (p = 0.7) or the expression of p53 (p = 0.5). In conclusion, thin AKs show the same severity of dysplasia and expression of p53 as thicker AK lesions. Consequently, clinical thickness cannot predict aggressiveness.
Aberrant Meiotic Prophase I Leads to Genic Male Sterility in the Novel TE5A Mutant of Brassica napus
Authors: Yan Xiaohong , Zeng Xinhua , Wang Shasha , Li Keqi , Yuan Rong , Gao Hongfei , Luo Junling , Liu Fang , Wu Yuhua , Li Yunjing , Zhu Li , Wu Gang 
Published: September 2016

AbstractGenic male sterility (GMS) has already been extensively utilized for hybrid rapeseed production. TE5A is a novel thermo-sensitive dominant GMS line in Brassica napus, however, its mechanisms of GMS remain largely unclear. Histological and Transmission electron microscopy (TEM) analyses of anthers showed that the male gamete development of TE5A was arrested at meiosis prophase I. EdU uptake of S-phase meiocytes revealed that the TE5A mutant could accomplish DNA replication, however, chromosomal and fluorescence in situ hybridization (FISH) analyses of TE5A showed that homologous chromosomes could not pair, synapse, condense and form bivalents. We then analyzed the transcriptome differences between young floral buds of sterile plants and its near-isogenic fertile plants through RNA-Seq. A total of 3,841 differentially expressed genes (DEGs) were obtained, some of which were associated with homologous chromosome behavior and cell cycle control during meiosis. Dynamic expression changes of selected candidate DEGs were then analyzed at different anther developmental stages. The present study not only demonstrated that the TE5A mutant had defects in meiotic prophase I via detailed cytological analysis, but also provided a global insight into GMS-associated DEGs and elucidated the mechanisms of GMS in TE5A through RNA-Seq.
FAMSA: Fast and accurate multiple sequence alignment of huge protein families
Authors: Deorowicz Sebastian , Debudaj-Grabysz Agnieszka , Gudyś Adam 
Published: September 2016

AbstractRapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilization of the longest common subsequence measure for determining pairwise similarities, a novel method of evaluating gap costs, and a new iterative refinement scheme. What matters is that its implementation is highly optimized and parallelized to make the most of modern computer platforms. Thanks to the above, quality indicators, i.e. sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms, such as Clustal Omega or MAFFT for datasets exceeding a few thousand sequences. Quality does not compromise on time or memory requirements, which are an order of magnitude lower than those in the existing solutions. For example, a family of 415519 sequences was analyzed in less than two hours and required no more than 8 GB of RAM. FAMSA is available for free at http://sun.aei.polsl.pl/REFRESH/famsa.