bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fission of Lipid-Vesicles by Membrane Phase Transitions in Thermal Convection
Authors: Kudella Patrick W. , Preißinger Katharina , Morasch Matthias , Dirscherl Christina F. , Braun Dieter , Wixforth Achim , Westerhausen Christoph 
Published: December 2019

AbstractUnilamellar lipid vesicles can serve as model for protocells. We present a vesicle fission mechanism in a thermal gradient under flow in a convection chamber, where vesicles cycle cold and hot regions periodically. Crucial to obtain fission of the vesicles in this scenario is a temperature-induced membrane phase transition that vesicles experience multiple times. We model the temperature gradient of the chamber with a capillary to study single vesicles on their way through the temperature gradient in an external field of shear forces. Starting in the gel-like phase the spherical vesicles are heated above their main melting temperature resulting in a dumbbell-deformation. Further downstream a temperature drop below the transition temperature induces splitting of the vesicles without further physical or chemical intervention. This mechanism also holds for less cooperative systems, as shown here for a lipid alloy with a broad transition temperature width of 8 K. We find a critical tether length that can be understood from the transition width and the locally applied temperature gradient. This combination of a temperature-induced membrane phase transition and realistic flow scenarios as given e.g. in a white smoker enable a fission mechanism that can contribute to the understanding of more advanced protocell cycles.
The perceptual continuity field is retinotopic
Authors: Collins Thérèse 
Published: December 2019

AbstractVisual perception is systematically biased towards input from the recent past: perceived orientation, numerosity, and face identity are pulled towards previously seen stimuli. To better understand the brain level at which serial dependence occurs, the present study examined its spatial tuning. In three experiments, serial dependence occurred between stimuli occupying the same retinal position. Serial dependence between stimuli at distant retinal locations was smaller, even when the stimuli occupied the same location in external space. The spatial window over which serial dependence occurs is thus retinotopic, but wide, suggesting that serial dependence occurs at late stages of visual processing.
High efficiency DBR assisted grating chirp generators for silicon nitride fiber-chip coupling
Authors: Nambiar Siddharth , Ranganath Praveen , Kallega Rakshitha , Selvaraja Shankar Kumar 
Published: December 2019

AbstractSilicon Nitride (SiN) is emerging as a promising material for a variety of integrated photonic applications. Given its low index contrast however, a key challenge remains to design efficient couplers for the numerous platforms in SiN photonics portfolio. Using a combination of bottom reflector and a chirp generating algorithm, we propose and demonstrate high efficiency, grating couplers on two distinct SiN platforms. For a partially etched grating on 500 nm thick SiN, a calculated peak efficiency of −0.5 dB/coupler is predicted, while for a fully etched grating on 400 nm thick SiN, an efficiency of −0.4 dB/coupler is predicted. Experimentally measured coupling efficiencies are observed to be −1.17 and −1.24 dB/coupler for the partial and fully etched grating couplers respectively in the C-L band region. Furthermore, through numerical simulations, it is shown that the chirping algorithm can be implemented in eight additional combinations comprising SiN film thickness between 300–700 nm as well as alternate claddings, to achieve a per coupler loss between −0.33 to −0.65 dB.
A higher throughput assay for quantification of melphalan-induced DNA damage in peripheral blood mononuclear cells
Authors: van Kan Maia , Burns Kathryn E. , Browett Peter , Helsby Nuala A. 
Published: December 2019

AbstractInter-individual differences in DNA adduct formation and repair influence the response to melphalan treatment, however, further clinical investigation of this variability requires a logistically feasible and reproducible bioassay. Our improved fluorescence-based QPCR-block assay is robust, has good precision, and improved throughput. It also incorporates direct PCR amplification from melphalan exposed PBMC using commercially available blood tubes and extraction kits to maximise the utility of this assay for future clinical studies. Using this assay we have demonstrated reproducible inter-individual differences in melphalan-induced QPCR-block across individual PBMC donors. As proof-of-principle we assessed nine healthy donors and found a 7.8 fold range in sensitivity following exposure of PBMC ex vivo. This likely reflects differences in melphalan transport into cells as well as differences in DNA adduct repair proficiency. This improved bioassay may be useful for assessment of these processes in patients about to receive melphalan treatment.
Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels
Authors: Pakstis Andrew J. , Speed William C. , Soundararajan Usha , Rajeevan Haseena , Kidd Judith R. , Li Hui , Kidd Kenneth K. 
Published: December 2019

AbstractThe benefits of ancestry informative SNP (AISNP) panels can best accrue and be properly evaluated only as sufficient reference population data become readily accessible. Ideally the set of reference populations should approximate the genetic diversity of human populations worldwide. The Kidd and Seldin AISNP sets are two panels that have separately accumulated thus far the largest and most diverse collections of data on human reference populations from the major continental regions. A recent tally in the ALFRED allele frequency database finds 164 reference populations available for all the 55 Kidd AISNPs and 132 reference populations for all the 128 Seldin AISNPs. Although much more of the genetic diversity in human populations around the world still needs to be documented, 81 populations have genotype data available for all 170 AISNPs in the union of the Kidd and Seldin panels. In this report we examine admixture and principal component analyses on these 81 worldwide populations and some regional subsets of these reference populations to determine how well the combined panel illuminates population relationships. Analyses of this dataset that focused on Native American populations revealed very strong cluster patterns associated with many of the individual populations studied.
VAS2870 and VAS3947 attenuate platelet activation and thrombus formation via a NOX-independent pathway downstream of PKC
Authors: Lu Wan Jung , Li Jiun Yi , Chen Ray Jade , Huang Li Ting , Lee Tzu Yin , Lin Kuan Hung 
Published: December 2019

AbstractNADPH oxidase (NOX) enzymes are involved in a various physiological and pathological processes such as platelet activation and inflammation. Interestingly, we found that the pan-NOX inhibitors VAS compounds (VAS2870 and its analog VAS3947) exerted a highly potent antiplatelet effect. Unlike VAS compounds, concurrent inhibition of NOX1, 2, and 4 by treatment with ML171, GSK2795039, and GKT136901/GKT137831 did not affect thrombin and U46619-induced platelet aggregation. These findings suggest that VAS compounds may inhibit platelet aggregation via a NOX-independent manner. Thus, we aimed to investigate the detailed antiplatelet mechanisms of VAS compounds. The data revealed that VAS compounds blocked various agonist-induced platelet aggregation, possibly via blocking PKC downstream signaling, including IKKβ and p38 MAPK, eventually reducing platelet granule release, calcium mobilization, and GPIIbIIIa activation. In addition, VAS compounds inhibited mouse platelet aggregation-induced by collagen and thrombin. The in vivo study also showed that VAS compounds delayed thrombus formation without affecting normal hemostasis. This study is the first to demonstrate that, in addition to inhibiting NOX activity, VAS compounds reduced platelet activation and thrombus formation through a NOX-independent pathway downstream of PKC. These findings also indicate that VAS compounds may be safe and potentially therapeutic agents for treating patients with cardiovascular diseases.
Mutant IDH1 confers resistance to energy stress in normal biliary cells through PFKP-induced aerobic glycolysis and AMPK activation
Authors: Fujiwara Hiroaki , Tateishi Keisuke , Misumi Kento , Hayashi Akimasa , Igarashi Kaori , Kato Hiroyuki , Nakatsuka Takuma , Suzuki Nobumi , Yamamoto Keisuke , Kudo Yotaro , Hayakawa Yoku , Nakagawa Hayato , Tanaka Yasuo , Ijichi Hideaki , Kogure Hirofumi , Nakai Yosuke , Isayama Hiroyuki , Hasegawa Kiyoshi , Fukayama Masashi , Soga Tomoyoshi , Koike Kazuhiko 
Published: December 2019

AbstractMetabolism is a critical regulator of cell fate determination. Recently, the significance of metabolic reprogramming in environmental adaptation during tumorigenesis has attracted much attention in cancer research. Recurrent mutations in the isocitrate dehydrogenase (IDH) 1 or 2 genes have been identified in several cancers, including intrahepatic cholangiocarcinoma (ICC). Mutant IDHs convert α-ketoglutarate (α-KG) to 2-hydroxyglutarate (2-HG), which affects the activity of multiple α-KG-dependent dioxygenases including histone lysine demethylases. Although mutant IDH can be detected even in the early stages of neoplasia, how IDH mutations function as oncogenic drivers remains unclear. In this study, we aimed to address the biological effects of IDH1 mutation using intrahepatic biliary organoids (IBOs). We demonstrated that mutant IDH1 increased the formation of IBOs as well as accelerated glucose metabolism. Gene expression analysis and ChIP results revealed the upregulation of platelet isoform of phosphofructokinase-1 (PFKP), which is a rate-limiting glycolytic enzyme, through the alteration of histone modification. Knockdown of the Pfkp gene alleviated the mutant IDH1-induced increase in IBO formation. Notably, the high expression of PFKP was observed more frequently in patients with IDH-mutant ICC compared to in those with wild-type IDH (p < 0.01, 80.9% vs. 42.5%, respectively). Furthermore, IBOs expressing mutant IDH1 survived the suppression of ATP production caused by growth factor depletion and matrix detachment by retaining high ATP levels through 5ʹ adenosine monophosphate-activated protein kinase (AMPK) activation. Our findings provide a systematic understanding as to how mutant IDH induces tumorigenic preconditioning by metabolic rewiring in intrahepatic cholangiocytes.
Differential regulation of TRP channel gene and protein expression by intervertebral disc degeneration and back pain
Authors: Sadowska A. , Hitzl W. , Karol A. , Jaszczuk P. , Cherif H. , Haglund L. , Hausmann O. N. , Wuertz-Kozak K. 
Published: December 2019

AbstractIntervertebral disc (IVD) degeneration and consequent low back pain (LBP) are common and costly pathological processes that require improved treatment strategies. Transient Receptor Potential (TRP) channels constitute a family of multimodal ion channels that have recently emerged as contributors to disc pathologies and were thus proposed as potential therapeutic targets, although limited data on their presence and function in the IVD exist. The purpose of this study was to determine the mRNA and protein expression of TRP channels in non-degenerated and degenerated human IVD tissue (with different pain intensity and chronicity) using gene array, conventional qPCR and immunohistochemistry. We could demonstrate that 26 out of 28 currently known TRP channels are expressed in the IVD on the mRNA level, thereby revealing novel therapeutic candidates from the TRPC, TRPM and TRPML subfamilies. TRPC6, TRPM2 and TRPML1 displayed enhanced gene and protein expression in degenerated IVDs as compared to non-degenerated IVDs. Additionally, the gene expression of TRPC6 and TRPML1 was influenced by the IVD degeneration grade. Pain intensity and/or chronicity influenced the gene and/or protein expression of TRPC6, TRPM2 and TRML1. Interestingly, decreased gene expression of TRPM2 was observed in patients treated with steroids. This study supports the importance of TRP channels in IVD homeostasis and pathology and their possible application as pharmacological targets for the treatment of IVD degeneration and LBP. However, the exact function and activation of the highlighted TRP channels will have to be determined in future studies.
Unmixing noisy co-registered spectrum images of multicomponent nanostructures
Authors: Braidy Nadi , Gosselin Ryan 
Published: December 2019

AbstractAnalytical electron microscopy plays a key role in the development of novel nanomaterials. Electron energy-loss spectroscopy (EELS) and energy-dispersive X-ray spectroscopy (EDX) datasets are typically processed to isolate the background-subtracted elemental signal. Multivariate tools have emerged as powerful methods to blindly map the components, which addresses some of the shortcomings of the traditional methods. Here, we demonstrate the superior performance of a new multivariate optimization method using a challenging EELS and EDX dataset. The dataset was recorded from a spectrum image P-type metal-oxide-semiconductor stack with 7 components exhibiting heavy spectral overlap and a low signal-to-noise ratio. Compared to peak integration, independent component analysis, Baysian Linear Unmixing and Non-negative matrix factorization, the method proposed was the only one to identify the EELS spectra of all 7 components with the corresponding abundance profiles. Using the abundance of each component, it was possible to retrieve the EDX spectra of all the components, which were otherwise impossible to isolate, regardless of the method used. We expect that this robust method will bring a significant improvement for the chemical analysis of nanomaterials, especially for weak signals, dose-sensitive specimen or signals suffering heavy spectral overlap.
A comparative study on droplet characteristics and specific charge of ethanol in two small-scale electrospray systems
Authors: Gan Yunhua , Jiang Zhengwei , Li Haige , Luo Yanlai , Chen Xiaowen , Shi Yanling , Yan Yuying , Yan Yunfei 
Published: December 2019

AbstractAn investigation on the droplet characteristics of ethanol in small-scale combustors with two different systems was conducted experimentally and theoretically. The classical capillary-mesh electrode arrangement was applied in Type A electrospray system, and for Type B, an additional ring electrode is included. The droplet size and velocity were measured by a Phase Doppler Anemometer. The electric filed intensity was theoretically calculated in the two electrospray systems. Compared with Type A, Type B system has smaller droplet size and velocity in the same spraying mode. Meanwhile the electrospray process in Type B system is more stable than that in Type A with its smaller root mean square velocity. By measuring the spraying current, the average specific charge of the droplets for the two systems was obtained in different spraying modes. And it was found that the addition of the ring electrode can help to increase the droplet charge, which is the fundamental reason for Type B electrospray system to perform better. The corona charge of the droplets was theoretically calculated for the two electrospray systems. It was found that the calculated specific charge generated by corona charging was in good agreement with the experimental results.
Performance of tropical forest seedlings under shade and drought: an interspecific trade-off in demographic responses
Authors: Kupers Stefan J. , Wirth Christian , Engelbrecht Bettina M. J. , Hernández Andrés , Condit Richard , Wright S. Joseph , Rüger Nadja 
Published: December 2019

AbstractSeedlings in moist tropical forests must cope with deep shade and seasonal drought. However, the interspecific relationship between seedling performance in shade and drought remains unsettled. We quantified spatiotemporal variation in shade and drought in the seasonal moist tropical forest on Barro Colorado Island (BCI), Panama, and estimated responses of naturally regenerating seedlings as the slope of the relationship between performance and shade or drought intensity. Our performance metrics were relative height growth and first-year survival. We investigated the relationship between shade and drought responses for up to 63 species. There was an interspecific trade-off in species responses to shade versus species responses to dry season intensity; species that performed worse in the shade did not suffer during severe dry seasons and vice versa. This trade-off emerged in part from the absence of species that performed particularly well or poorly in both drought and shade. If drought stress in tropical forests increases with climate change and as solar radiation is higher during droughts, the trade-off may reinforce a shift towards species that resist drought but perform poorly in the shade by releasing them from deep shade.
Structural studies of the MMP-3 interaction with triple-helical collagen introduce new roles for the enzyme in tissue remodelling
Authors: Manka Szymon W. , Bihan Dominique , Farndale Richard W. 
Published: December 2019

AbstractMatrix metalloproteinase-3 (MMP-3) participates in normal extracellular matrix turnover during embryonic development, organ morphogenesis and wound healing, and in tissue-destruction associated with aneurysm, cancer, arthritis and heart failure. Despite its inability to cleave triple-helical collagens, MMP-3 can still bind to them, but the mechanism, location and role of binding are not known. We used the Collagen Toolkits, libraries of triple-helical peptides that embrace the entire helical domains of collagens II and III, to map MMP-3 interaction sites. The enzyme recognises five sites on collagen II and three sites on collagen III. They share a glycine-phenylalanine-hydroxyproline/alanine (GFO/A) motif that is recognised by the enzyme in a context-dependent manner. Neither MMP-3 zymogen (proMMP-3) nor the individual catalytic (Cat) and hemopexin (Hpx) domains of MMP-3 interact with the peptides, revealing cooperative binding of both domains to the triple helix. The Toolkit binding data combined with molecular modelling enabled us to deduce the putative collagen-binding mode of MMP-3, where all three collagen chains make contacts with the enzyme in the valley running across both Cat and Hpx domains. The observed binding pattern casts light on how MMP-3 could regulate collagen turnover and compete with various collagen-binding proteins regulating cell adhesion and proliferation.
Preparation and Characterization of Microencapsulated Ethylenediamine with Epoxy Resin for Self-healing Composites
Authors: Yuan Liye , Sun Tongqing , Hu Honglin , Yuan Shuxia , Yang Yu , Wang Rongguo , Lyu Chunxiang , Yang Fan , Lyu Xiaoxuan 
Published: December 2019

AbstractHealing agent microcapsules have been used to realize self-healing for polymeric composites. In this work a novel kind of microcapsules encapsulating ethylenediamine (EDA) with epoxy resin as shell material were prepared by interfacial polymerization technology. The oil phase was epoxy resin prepolymer and carbon tetrachloride, and the water phase was EDA and deionized water. Under the action of emulsifier, a stable water-in-oil emulsion was formed. Then the emulsion was added to dimethyl silicone oil, stirred and dispersed, to prepare microcapsules. In addition, the factors affecting the preparation of microcapsules were studied. In this study, Fourier transform infrared(FTIR) was carried out to demonstrate the chemical structure of ethylenediamine microcapsules. Optical microscope(OM) and scanning electron microscope(SEM) were used to observe the morphology of microcapsules. Thermogravimetric analysis and differential scanning calorimetry were done to investigate the thermal properties of microcapsules. Permeability experiment and isothermal aging test were executed to verify the environment resistance of microcapsules. Results showed that EDA was successfully coated in epoxy resin and the microcapsule size was in the range of 50~630 μm. The synthesized microcapsules were thermally stable below 75 °C and perfect permeability resistance to ethanol solvent.
Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn’s disease
Authors: Kowalska-Duplaga Kinga , Gosiewski Tomasz , Kapusta Przemysław , Sroka-Oleksiak Agnieszka , Wędrychowicz Andrzej , Pieczarkowski Stanisław , Ludwig-Słomczyńska Agnieszka H. , Wołkow Paweł P. , Fyderek Krzysztof 
Published: December 2019

AbstractThe aetiology of inflammatory bowel diseases (IBD) seems to be strongly connected to changes in the enteral microbiome. The dysbiosis pattern seen in Crohn’s disease (CD) differs among published studies depending on patients’ age, disease phenotype and microbiome research methods. The aims was to investigate microbiome in treatment-naive paediatric patients to get an insight into its structure at the early stage of the disease in comparison to healthy. Stool samples were obtained from controls and newly diagnosed patients prior to any intervention. Microbiota was analysed by 16SrRNAnext-generation-sequencing (NGS). Differences in the within-sample phylotype richness and evenness (alpha diversity) were detected between controls and patients. Statistically significant dissimilarities between samples were present for all used metrics. We also found a significant increase in the abundance of OTUs of theEnterococcusgenus and reduction in, among others,Bifidobacterium(B. adolescentis),Roseburia (R.faecis), Faecalibacterium (F. prausnitzii), Gemmiger (G. formicilis), Ruminococcus (R. bromii) and Veillonellaceae (Dialister). Moreover, differences in alpha and beta diversities in respect to calprotectin and PCDAI were observed: patients with calprotectin <100 µg/g and with PCDAI below 10 points vs those with calprotectin >100 µg/g and mild (10–27.7 points), moderate (27.5–40 points) or severe (>40 points) CD disease activity had higher richness and diversity of gut microbiota. The results of our study highlight reduced diversity and dysbiosis at the earliest stage of the disease. Microbial imbalance and low abundance of butyrate-producing bacteria, includingBifidobacterium adolescentis, may suggest benefits of microbial modification therapy.
Overexpression of LAPTM4B-35 is a negative prognostic factor in head and neck squamous cell carcinoma
Authors: Kotowski Ulana , Kadletz Lorenz , Schneider Sven , Oberndorfer Felicitas , Schnoell Julia , Gurnhofer Elisabeth , Kenner Lukas , Lucas Trevor , Heiduschka Gregor 
Published: December 2019

AbstractOverexpression of LAPTM4B-35 (lysosomal-associated transmembrane protein 4β-35) is associated with a poor prognosis in numerous malignant tumours. Expression patterns and effects of LAPTM4B-35 on head and neck squamous cell carcinomas (HNSCC) are unknown. The aim of this study was to investigate the prognostic relevance of LAPTM4B-35 in HNSCC. Tissue microarrays were constructed with primary tumours and associated lymph node metastases isolated from 127 patients. The expression of LAPTM4B-35 was investigated by immunohistochemistry and the results were correlated with survival data. LAPTM4B-35 in the primary tumour was highly expressed in 47.2% of the patients (60/127). LAPTM4B-35 expression was significantly associated with tumour stage. Moreover, overexpression of LAPTM4B-35 correlated with a significantly worse disease-free survival (10.23 years vs. not reached) and a higher recurrence rate (40.7% vs. 25%). High expression of LAPTM4B-35 in lymph node metastasis was found in 29.2% of cases. In 19.4% of cases, high LAPTM4B-35 expression was observed in both the primary tumour and corresponding lymph node metastases. In conclusion, our data indicates that overexpression of LAPTM4B-35 is associated with poor prognosis and may therefore serve as a new prognostic marker in HNSCC.