bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D microtumors in vitro supported by perfused vascular networks
Authors: Sobrino Agua , Phan Duc T. T. , Datta Rupsa , Wang Xiaolin , Hachey Stephanie J. , Romero-López Mónica , Gratton Enrico , Lee Abraham P. , George Steven C. , Hughes Christopher C. W. 
Published: August 2016

AbstractThere is a growing interest in developing microphysiological systems that can be used to model both normal and pathological human organs in vitro. This “organs-on-chips” approach aims to capture key structural and physiological characteristics of the target tissue. Here we describe in vitro vascularized microtumors (VMTs). This “tumor-on-a-chip” platform incorporates human tumor and stromal cells that grow in a 3D extracellular matrix and that depend for survival on nutrient delivery through living, perfused microvessels. Both colorectal and breast cancer cells grow vigorously in the platform and respond to standard-of-care therapies, showing reduced growth and/or regression. Vascular-targeting agents with different mechanisms of action can also be distinguished, and we find that drugs targeting only VEGFRs (Apatinib and Vandetanib) are not effective, whereas drugs that target VEGFRs, PDGFR and Tie2 (Linifanib and Cabozantinib) do regress the vasculature. Tumors in the VMT show strong metabolic heterogeneity when imaged using NADH Fluorescent Lifetime Imaging Microscopy and, compared to their surrounding stroma, many show a higher free/bound NADH ratio consistent with their known preference for aerobic glycolysis. The VMT platform provides a unique model for studying vascularized solid tumors in vitro.
Use of Bayesian Inference in Crystallographic Structure Refinement via Full Diffraction Profile Analysis
Authors: Fancher Chris M. , Han Zhen , Levin Igor , Page Katharine , Reich Brian J. , Smith Ralph C. , Wilson Alyson G. , Jones Jacob L. 
Published: August 2016

AbstractA Bayesian inference method for refining crystallographic structures is presented. The distribution of model parameters is stochastically sampled using Markov chain Monte Carlo. Posterior probability distributions are constructed for all model parameters to properly quantify uncertainty by appropriately modeling the heteroskedasticity and correlation of the error structure. The proposed method is demonstrated by analyzing a National Institute of Standards and Technology silicon standard reference material. The results obtained by Bayesian inference are compared with those determined by Rietveld refinement. Posterior probability distributions of model parameters provide both estimates and uncertainties. The new method better estimates the true uncertainties in the model as compared to the Rietveld method.
Kremen1 regulates mechanosensory hair cell development in the mammalian cochlea and the zebrafish lateral line
Authors: Mulvaney Joanna F. , Thompkins Cathrine , Noda Teppei , Nishimura Koji , Sun Willy W. , Lin Shuh-Yow , Coffin Allison , Dabdoub Alain 
Published: August 2016

AbstractHere we present spatio-temporal localization of Kremen1, a transmembrane receptor, in the mammalian cochlea and investigate its role in the formation of sensory organs in mammal and fish model organisms. We show that Kremen1 is expressed in prosensory cells during cochlear development and in supporting cells of the adult mouse cochlea. Based on this expression pattern, we investigated whether Kremen1 functions to modulate cell fate decisions in the prosensory domain of the developing cochlea. We used gain and loss-of-function experiments to show that Kremen1 is sufficient to bias cells towards supporting cell fate and is implicated in suppression of hair cell formation. In addition to our findings in the mouse cochlea, we examined the effects of over expression and loss of Kremen1 in the zebrafish lateral line. In agreement with our mouse data, we show that over expression of Kremen1 has a negative effect on the number of mechanosensory cells that form in the zebrafish neuromasts and that fish lacking Kremen1 protein develop more hair cells per neuromast compared to wild type fish. Collectively, these data support an inhibitory role for Kremen1 in hair cell fate specification.
Optically pumped subwavelength-scale metallodielectric nanopatch resonators
Authors: Kwon Kyungmok , You Jong-bum , Shim Jaeho , Jung Youngho , Yu Kyoungsik 
Published: August 2016

AbstractWe discuss subwavelength-scale semiconductor metal-optic resonators placed on the metal substrate with various top metal plate sizes. Albeit with large optical losses, addition of metal layers converts a leaky semiconductor nano-block into a highly-confined optical cavity. Optically pumped lasing action is observed with the extended top metal layer that can significantly suppress the radiation losses. Careful investigation of self-heating effects during the optical carrier injection process shows the importance of temperature-dependent material properties in the laser rate equation model and the overall laser performances.
Soil bacterial and fungal community dynamics in relation to Panax notoginseng death rate in a continuous cropping system
Authors: Dong Linlin , Xu Jiang , Feng Guangquan , Li Xiwen , Chen Shilin 
Published: August 2016

AbstractNotoginseng (Panax notoginseng), a valuable herbal medicine, has high death rates in continuous cropping systems. Variation in the soil microbial community is considered the primary cause of notoginseng mortality, although the taxa responsible for crop failure remains unidentified. This study used high-throughput sequencing methods to characterize changes in the microbial community and screen microbial taxa related to the death rate. Fungal diversity significantly decreased in soils cropped with notoginseng for three years. The death rate and the fungal diversity were significantly negatively correlated, suggesting that fungal diversity might be a potential bioindicator of soil health. Positive correlation coefficients revealed that Burkholderiales, Syntrophobacteraceae, Myrmecridium, Phaeosphaeria, Fusarium and Phoma were better adapted to colonization of diseased plants. The relative abundance of Fusarium oxysporum (R = 0.841, P < 0.05) and Phaeosphaeria rousseliana (R = 0.830, P < 0.05) were positively associated with the death rate. F. oxysporum was a pathogen of notoginseng root-rot that caused seedling death. Negative correlation coefficients indicated that Thermogemmatisporaceae, Actinosynnemataceae, Hydnodontaceae, Herpotrichiellaceae and Coniosporium might be antagonists of pathogens and the relative abundance of Coniosporium perforans was negatively correlated with the death rate. Our findings provide a dynamic overview of the microbial community and present a clear scope for screening beneficial microbes and pathogens of notoginseng.
Extracellular Vesicles from Metastatic Rat Prostate Tumors Prime the Normal Prostate Tissue to Facilitate Tumor Growth
Authors: Halin Bergström Sofia , Hägglöf Christina , Thysell Elin , Bergh Anders , Wikström Pernilla , Lundholm Marie 
Published: August 2016

AbstractAccumulating data indicates that tumor-derived extracellular vesicles (EVs) are responsible for tumor-promoting effects. However, if tumor EVs also prepare the tumor-bearing organ for subsequent tumor growth and if this effect is different in low and high malignant tumors is not thoroughly explored. Here we used orthotopic rat Dunning R-3327 prostate tumors to compare the role of EVs from fast growing and metastatic MatLyLu (MLL) tumors with EVs from more indolent and non-metastatic Dunning G (G) tumors. Prostate tissue pre-conditioned with MLL-EVs in vivo facilitated G tumor establishment compared to G-EVs. MLL-EVs increased prostate epithelial proliferation and macrophage infiltration into the prostate compared to G-EVs. Both types of EVs increased macrophage endocytosis and the mRNA expression of genes associated with M2 polarization in vitro, with MLL-EVs giving the most pronounced effects. MLL-EVs also altered the mRNA expression of growth factors and cytokines in primary rat prostate fibroblasts compared to G-EVs, suggesting fibroblast activation. Our findings propose that EVs from metastatic tumors have the ability to prime the prostate tissue and enhance tumor growth to a higher extent than EVs from non-metastatic tumors. Identifying these differences could lead to novel therapeutic targets and potential prognostic markers for prostate cancer.
Self-organized sorting limits behavioral variability in swarms
Authors: Copenhagen Katherine , Quint David A. , Gopinathan Ajay 
Published: August 2016

AbstractSwarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters.
Fabrication of Long-Term Underwater Superoleophobic Al Surfaces and Application on Underwater Lossless Manipulation of Non-Polar Organic Liquids
Authors: Song Jinlong , Huang Liu , Lu Yao , Liu Xin , Deng Xu , Yang Xiaolong , Huang Shuai , Sun Jing , Jin Zhuji , Parkin Ivan P. 
Published: August 2016

AbstractUnderwater superoleophobic surfaces have different applications in fields from oil/water separation to underwater lossless manipulation. This kind of surfaces can be easily transformed from superhydrophilic surfaces in air, which means the stability of superhydrophilicity in air determines the stability of underwater superoleophobicity. However, superhydrophilic surfaces fabricated by some existing methods easily become hydrophobic or superhydrophobic in air with time. Here, a facile method combined with electrochemical etching and boiling water immersion is developed to fabricate long-term underwater superoleophobic surfaces. The surface morphologies and chemical compositions are investigated. The results show that the electrochemically etched and boiling-water immersed Al surfaces have excellent long-term superhydrophilicity in air for over 1 year and boehmite plays an important role in maintaining long-term stability of wettability. Based on the fabricated underwater superoleophobic surfaces, a special method and device were developed to realize the underwater lossless manipulation of immiscible organic liquid droplets with a large volume. The capture and release of liquid droplets were realized by controlling the resultant force of the applied driving pressure, gravity and buoyancy. The research has potential application in research-fields such as the transfer of valuable reagents, accurate control of miniature chemical reactions, droplet-based reactors, and eliminates contamination of manipulator components.
Floquet edge states in germanene nanoribbons
Authors: Tahir M. , Zhang Q. Y. , Schwingenschlögl U. 
Published: August 2016

AbstractWe theoretically demonstrate versatile electronic properties of germanene monolayers under circularly, linearly and elliptically polarized light. We show for the high frequency regime that the edge states can be controlled by tuning the amplitude of the light and by applying a static electric field. For circularly polarized light the band gap in one valley is reduced and in the other enhanced, enabling single valley edge states. For linearly polarized light spin-split states are found for both valleys, being connected by time reversal symmetry. The effects of elliptically polarized light are similar to those of circularly polarized light. The transport properties of zigzag nanoribbons in the presence of disorder confirm a nontrivial nature of the edge states under circularly and elliptically polarized light.
Molecular and ionic-scale chemical mechanisms behind the role of nitrocyl group in the electrochemical removal of heavy metals from sludge
Authors: Hasan S. W. , Ahmed I. , Housani A. A. , Giwa A. 
Published: August 2016

AbstractThe chemical basis for improved removal rates of toxic heavy metals such as Zn and Cu from wastewater secondary sludge has been demonstrated in this study. Instead of using excess corrosive chemicals as the source of free nitrous acid (FNA) for improved solubility of heavy metals in the sludge (in order to enhance electrokinetics), an optimized use of aqua regia has been proposed as an alternative. Fragments of nitrocyl group originated from aqua regia are responsible for the disruption of biogenic mixed liquor volatile suspended solids (MLVSS) and this disruption resulted in enhanced removal of exposed and oxidized metal ions. A diversity of nitric oxide (NO), peroxy nitrous acid, and peroxy nitroso group are expected to be introduced in the mixed liquor by the aqua regia for enhanced electrochemical treatment. The effects of pectin as a post treatment on the Zn removal from sludge were also presented for the first time. Results revealed 63.6% Cu and 93.7% Zn removal efficiencies, as compared to 49% Cu and 74% Zn removal efficiencies reported in a recent study. Also, 93.3% reduction of time-to-filter (TTF), and 95 mL/g of sludge volume index (SVI) were reported. The total operating cost obtained was USD 1.972/wet ton.
Epithelial-mesenchymal transition-associated microRNA/mRNA signature is linked to metastasis and prognosis in clear-cell renal cell carcinoma
Authors: Mlcochova Hana , Machackova Tana , Rabien Anja , Radova Lenka , Fabian Pavel , Iliev Robert , Slaba Katerina , Poprach Alexandr , Kilic Ergin , Stanik Michal , Redova-Lojova Martina , Svoboda Marek , Dolezel Jan , Vyzula Rostislav , Jung Klaus , Slaby Ondrej 
Published: August 2016

AbstractClear-cell renal cell carcinomas (ccRCCs) are genetically heterogeneous tumors presenting diverse clinical courses. Epithelial-mesenchymal transition (EMT) is a crucial process involved in initiation of metastatic cascade. The aim of our study was to identify an integrated miRNA/mRNA signature associated with metastasis and prognosis in ccRCC through targeted approach based on analysis of miRNAs/mRNAs associated with EMT. A cohort of 230 ccRCC was included in our study and further divided into discovery, training and validation cohorts. EMT markers were evaluated in ccRCC tumor samples, which were grouped accordingly to EMT status. By use of large-scale miRNA/mRNA expression profiling, we identified miRNA/mRNA with significantly different expression in EMT-positive tumors and selected 41 miRNAs/mRNAs for training phase of the study to evaluate their diagnostic and prognostic potential. Fifteen miRNAs/mRNAs were analyzed in the validation phase, where all evaluated miRNA/mRNA candidates were confirmed to be significantly deregulated in tumor tissue. Some of them significantly differed in metastatic tumors, correlated with clinical stage, with Fuhrman grade and with overall survival. Further, we established an EMT-based stage-independent prognostic scoring system enabling identification of ccRCC patients at high-risk of cancer-related death. Finally, we confirmed involvement of miR-429 in EMT regulation in RCC cells in vitro.
Charge and spin transport in single and packed ruthenium-terpyridine molecular devices: Insight from first-principles calculations
Authors: Morari C. , Buimaga-Iarinca L. , Rungger I. , Sanvito S. , Melinte S. , Rignanese G.-M. 
Published: August 2016

AbstractUsing first-principles calculations, we study the electronic and transport properties of rutheniumterpyridine molecules sandwiched between two Au(111) electrodes. We analyse both single and packed molecular devices, more amenable to scaling and realistic integration approaches. The devices display all together robust negative differential resistance features at low bias voltages. Remarkably, the electrical control of the spin transport in the studied systems implies a subtle distribution of the magnetisation density within the biased devices and highlights the key role of the Au(111) electrical contacts.
Coral reef soundscapes may not be detectable far from the reef
Authors: Kaplan Maxwell B. , Mooney T. Aran 
Published: August 2016

AbstractBiological sounds produced on coral reefs may provide settlement cues to marine larvae. Sound fields are composed of pressure and particle motion, which is the back and forth movement of acoustic particles. Particle motion (i.e., not pressure) is the relevant acoustic stimulus for many, if not most, marine animals. However, there have been no field measurements of reef particle motion. To address this deficiency, both pressure and particle motion were recorded at a range of distances from one Hawaiian coral reef at dawn and mid-morning on three separate days. Sound pressure attenuated with distance from the reef at dawn. Similar trends were apparent for particle velocity but with considerable variability. In general, average sound levels were low and perhaps too faint to be used as an orientation cue except very close to the reef. However, individual transient sounds that exceeded the mean values, sometimes by up to an order of magnitude, might be detectable far from the reef, depending on the hearing abilities of the larva. If sound is not being used as a long-range cue, it might still be useful for habitat selection or other biological activities within a reef.
MiR-146b negatively regulates migration and delays progression of T-cell acute lymphoblastic leukemia
Authors: Correia Nádia C. , Fragoso Rita , Carvalho Tânia , Enguita Francisco J. , Barata João T. 
Published: August 2016

AbstractPrevious results indicated that miR-146b-5p is downregulated by TAL1, a transcription factor critical for early hematopoiesis that is frequently overexpressed in T-cell acute lymphoblastic leukemia (T-ALL) where it has an oncogenic role. Here, we confirmed that miR-146b-5p expression is lower in TAL1-positive patient samples than in other T-ALL cases. Furthermore, leukemia T-cells display decreased levels of miR-146b-5p as compared to normal T-cells, thymocytes and other hematopoietic progenitors. MiR-146b-5p silencing enhances the in vitro migration and invasion of T-ALL cells, associated with increased levels of filamentous actin and chemokinesis. In vivo, miR-146b overexpression in a TAL1-positive cell line extends mouse survival in a xenotransplant model of human T-ALL. In contrast, knockdown of miR-146b-5p results in leukemia acceleration and decreased mouse overall survival, paralleled by faster tumor infiltration of the central nervous system. Our results suggest that miR-146b-5p is a functionally relevant microRNA gene in the context of T-ALL, whose negative regulation by TAL1 and possibly other oncogenes contributes to disease progression by modulating leukemia cell motility and disease aggressiveness.
Examining how p16INK4a expression levels are linked to handgrip strength in the elderly
Authors: Kao Tung-Wei , Chen Wei-Liang , Han Der- Sheng , Huang Ying-Hsin , Chen Chi-Ling , Yang Wei-Shiung 
Published: August 2016

AbstractAlthough many studies have shown that p16INK4a is more highly expressed in the human body during senescence, studies on its relevance to handgrip strength among old adults, are relatively sparse. We enrolled 205 community-dwelling old adults aged 65 years and older without specific medical conditions. Handgrip strength of the dominant hand was measured. Low handgrip strength was defined as the lowest quartile of handgrip strength among the participants. RNA was extracted from peripheral white blood cells. Use quantitative polymerase chain reaction to estimate the p16INK4a mRNA expression level. The average handgrip strength was 25.22 ± 8.98 kg and gender difference was observed. In the linear regression model, the p16INK4a mRNA expression level was significantly negatively associated with handgrip strength in men but not in women. The β coefficient, representing the change of handgrip strength for each increment in the p16INK4a mRNA expression level, was −0.208 (p = 0.024) among old men. The negative association remained after additional covariates adjustment. In the multiple logistic regression model among old men, the odds ratio (OR) of low handgrip strength was 1.246 (p = 0.032). In this study, we observed the p16INK4a mRNA expression level was negative associated with handgrip strength among community-dwelling old men.
Scalable Production of Glioblastoma Tumor-initiating Cells in 3 Dimension Thermoreversible Hydrogels
Authors: Li Qiang , Lin Haishuang , Wang Ou , Qiu Xuefeng , Kidambi Srivatsan , Deleyrolle Loic P. , Reynolds Brent A. , Lei Yuguo 
Published: August 2016

AbstractThere is growing interest in developing drugs that specifically target glioblastoma tumor-initiating cells (TICs). Current cell culture methods, however, cannot cost-effectively produce the large numbers of glioblastoma TICs required for drug discovery and development. In this paper we report a new method that encapsulates patient-derived primary glioblastoma TICs and grows them in 3 dimension thermoreversible hydrogels. Our method allows long-term culture (~50 days, 10 passages tested, accumulative ~>1010-fold expansion) with both high growth rate (~20-fold expansion/7 days) and high volumetric yield (~2.0 × 107 cells/ml) without the loss of stemness. The scalable method can be used to produce sufficient, affordable glioblastoma TICs for drug discovery.
Human Ex-Vivo Liver Model for Acetaminophen-induced Liver Damage
Authors: Schreiter Thomas , Sowa Jan-Peter , Schlattjan Martin , Treckmann Jürgen , Paul Andreas , Strucksberg Karl-Heinz , Baba Hideo A. , Odenthal Margarete , Gieseler Robert K. , Gerken Guido , Arteel Gavin E. , Canbay Ali 
Published: August 2016

AbstractReliable test systems to identify hepatotoxicity are essential to predict unexpected drug-related liver injury. Here we present a human ex-vivo liver model to investigate acetaminophen-induced liver injury. Human liver tissue was perfused over a 30 hour period with hourly sampling from the perfusate for measurement of general metabolism and clinical parameters. Liver function was assessed by clearance of indocyanine green (ICG) at 4, 20 and 28 hours. Six pieces of untreated human liver specimen maintained stable liver function over the entire perfusion period. Three liver sections incubated with low-dose acetaminophen revealed strong damage, with ICG half-lives significantly higher than in non-treated livers. In addition, the release of microRNA-122 was significantly higher in acetaminophen-treated than in non-treated livers. Thus, this model allows for investigation of hepatotoxicity in human liver tissue upon applying drug concentrations relevant in patients.