bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms
Authors: Ghanbari Azadeh , Dehghany Jaber , Schwebs Timo , Müsken Mathias , Häussler Susanne , Meyer-Hermann Michael 
Published: September 2016

AbstractPseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data. Our simulations show colony formation by immotile cells. Motile cells escape from a single colony by nutrient chemotaxis and hence no mushroom shape develops. A high number density of non-motile colonies leads to migration of motile cells onto the top of the colonies and formation of mushroom-shaped structures. This model proposes that the formation of mushroom-shaped structures can be predicted by parameters at the time of bacteria inoculation. Depending on nutrient levels and the initial number density of stalks, mushroom-shaped structures only form in a restricted regime. This opens the possibility of early manipulation of spatial pattern formation in bacterial colonies, using environmental factors.
CD147/EMMPRIN overexpression and prognosis in cancer: A systematic review and meta-analysis
Authors: Xin Xiaoyan , Zeng Xianqin , Gu Huajian , Li Min , Tan Huaming , Jin Zhishan , Hua Teng , Shi Rui , Wang Hongbo 
Published: September 2016

AbstractCD147/EMMPRIN (extracellular matrix metalloproteinase inducer) plays an important role in tumor progression and a number of studies have suggested that it is an indicator of tumor prognosis. This current meta-analysis systematically reevaluated the predictive potential of CD147/EMMPRIN in various cancers. We searched PubMed and Embase databases to screen the literature. Fixed-effect and random-effect meta-analytical techniques were used to correlate CD147 expression with outcome measures. A total of 53 studies that included 68 datasets were eligible for inclusion in the final analysis. We found a significant association between CD147/EMMPRIN overexpression and adverse tumor outcomes, such as overall survival, disease-specific survival, progression-free survival, metastasis-free survival or recurrence-free survival, irrespective of the model analysis. In addition, CD147/EMMPRIN overexpression predicted a high risk for chemotherapy drugs resistance. CD147/EMMPRIN is a central player in tumor progression and predicts a poor prognosis, including in patients who have received chemo-radiotherapy. Our results provide the evidence that CD147/EMMPRIN could be a potential therapeutic target for cancers.
Possible recent warming hiatus on the northwestern Tibetan Plateau derived from ice core records
Authors: An Wenling , Hou Shugui , Zhang Wangbin , Wu Shuangye , Xu Hao , Pang Hongxi , Wang Yetang , Liu Yaping 
Published: September 2016

AbstractMany studies have reported enhanced warming trend on the Tibetan Plateau (TP), even during the warming hiatus period. However, most of these studies are based on instrumental data largely collected from the eastern TP, whereas the temperature trend over the extensive northwestern TP remains uncertain due to few meteorological stations. Here we combined the stable isotopic δ18O record of an ice core recovered in 2012 from the Chongce glacier with the δ18O records of two other ice cores (i.e., Muztagata and Zangser Kangri) in the same region to establish a regional temperature series for the northwestern TP. The reconstruction shows a significant warming trend with a rate of 0.74 ± 0.12 °C/decade for the period 1970–2000, but a decreasing trend from 2001 to 2012. This is consistent with the reduction of warming rates during the recent decade observed at the only two meteorological stations on the northwestern TP, even though most stations on the eastern TP have shown persistent warming during the same period. Our results suggest a possible recent warming hiatus on the northwestern TP. This could have contributed to the relatively stable status of glaciers in this region.
Complete androgen insensitivity syndrome caused by a deep intronic pseudoexon-activating mutation in the androgen receptor gene
Authors: Känsäkoski Johanna , Jääskeläinen Jarmo , Jääskeläinen Tiina , Tommiska Johanna , Saarinen Lilli , Lehtonen Rainer , Hautaniemi Sampsa , Frilander Mikko J. , Palvimo Jorma J. , Toppari Jorma , Raivio Taneli 
Published: September 2016

AbstractMutations in the X-linked androgen receptor (AR) gene underlie complete androgen insensitivity syndrome (CAIS), the most common cause of 46,XY sex reversal. Molecular genetic diagnosis of CAIS, however, remains uncertain in patients who show normal coding region of AR. Here, we describe a novel mechanism of AR disruption leading to CAIS in two 46,XY sisters. We analyzed whole-genome sequencing data of the patients for pathogenic variants outside the AR coding region. Patient fibroblasts from the genital area were used for AR cDNA analysis and protein quantification. Analysis of the cDNA revealed aberrant splicing of the mRNA caused by a deep intronic mutation (c.2450-118A>G) in the intron 6 of AR. The mutation creates a de novo 5′ splice site and a putative exonic splicing enhancer motif, which leads to the preferential formation of two aberrantly spliced mRNAs (predicted to include a premature stop codon). Patient fibroblasts contained no detectable AR protein. Our results show that patients with CAIS and normal AR coding region need to be examined for deep intronic mutations that can lead to pseudoexon activation.
Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa
Authors: Okada Chiaki , Wakabayashi Hiroko , Kobayashi Momoko , Shinoda Akira , Tanaka Isao , Yao Min 
Published: September 2016

AbstractLipid A (also known as endotoxin) is the hydrophobic portion of lipopolysaccharides. It is an essential membrane component required for the viability of gram-negative bacteria. The enzymes involved in its biosynthesis are attractive targets for the development of novel antibiotics. LpxH catalyzes the fourth step of the lipid A biosynthesis pathway and cleaves the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP. Here we present the structures of LpxH from Pseudomonas aeruginosa (PaLpxH). PaLpxH consists of two domains: a catalytic domain that is homologous to the metallophosphoesterases and a helical insertion domain. Lipid X was captured in the crevice between these two domains, with its phosphate group facing the dinuclear metal (Mn2+) center and two acyl chains buried in the hydrophobic cavity. The structures reveal that a large conformational change occurs at the lipid X binding site surface upon the binding/release of the product molecule. Based on these observations, we propose a novel model for lipid X embedding, which involves the scissor-like movement of helix α6, resulting in the release of lipid X into the lipid bilayer.
The effect of bilirubin on the excitability of mitral cells in the olfactory bulb of the rat
Authors: Chen Xiao-Juan , Zhou Hui-Qun , Ye Hai-bo , Li Chun-Yan , Zhang Wei-Tian 
Published: September 2016

AbstractOlfactory dysfunction is a common clinical phenomenon observed in various liver diseases. Previous studies have shown a correlation between smell disorders and bilirubin levels in patients with hepatic diseases. Bilirubin is a well-known neurotoxin; however, its effect on neurons in the main olfactory bulb (MOB), the first relay in the olfactory system, has not been examined. We investigated the effect of bilirubin (>3 μM) on mitral cells (MCs), the principal output neurons of the MOB. Bilirubin increased the frequency of spontaneous firing and the frequency but not the amplitude of spontaneous excitatory postsynaptic currents (sEPSCs). TTX completely blocked sEPSCs in almost all of the cells tested. Bilirubin activity was partially blocked by N-methyl-D-aspartate (NMDA) and α-amino-3-hydroxy-5-methyl-4-isoxazolepro pionic acid (AMPA) receptor antagonists. Furthermore, we found that bilirubin increased the frequency of intrinsic firing independent of synaptic transmission in MCs. Our findings suggest that bilirubin enhances glutamatergic transmission and strengthens intrinsic firing independent of synaptic transmission, all of which cause hyperexcitability in MCs. Our findings provide the basis for further investigation into the mechanisms underlying olfactory dysfunction that are often observed in patients with severe liver disease.
Plasmonic nanoantenna hydrophones
Authors: Maksymov Ivan S. , Greentree Andrew D. 
Published: September 2016

AbstractUltrasound is a valuable biomedical imaging modality and diagnostic tool. Here we theoretically demonstrate that a single dipole plasmonic nanoantenna can be used as an optical hydrophone for MHz-range ultrasound. The nanoantenna is tuned to operate on a high-order plasmon mode, which provides an increased sensitivity to ultrasound in contrast to the usual approach of using the fundamental dipolar plasmon resonance. Plasmonic nanoantenna hydrophones may be useful for ultrasonic imaging of biological cells, cancer tissues or small blood vessels, as well as for Brillouin spectroscopy at the nanoscale.
Ordered Peierls distortion prevented at growth onset of GeTe ultra-thin films
Authors: Wang Ruining , Campi Davide , Bernasconi Marco , Momand Jamo , Kooi Bart J. , Verheijen Marcel A. , Wuttig Matthias , Calarco Raffaella 
Published: September 2016

AbstractUsing reflection high-energy electron diffraction (RHEED), the growth onset of molecular beam epitaxy (MBE) deposited germanium telluride (GeTe) film on Si(111)-(√3 × √3)R30°-Sb surfaces is investigated, and a larger than expected in-plane lattice spacing is observed during the deposition of the first two molecular layers. High-resolution transmission electron microscopy (HRTEM) confirms that the growth proceeds via closed layers, and that those are stable after growth. The comparison of the experimental Raman spectra with theoretical calculated ones allows assessing the shift of the phonon modes for a quasi-free-standing ultra-thin GeTe layer with larger in-plane lattice spacing. The manifestation of the latter phenomenon is ascribed to the influence of the interface and the confinement of GeTe within the limited volume of material available at growth onset, either preventing the occurrence of Peierls dimerization or their ordered arrangement to occur normally.
24-hour-restraint stress induces long-term depressive-like phenotypes in mice
Authors: Chu Xixia , Zhou Ying , Hu Zhiqiang , Lou Jingyu , Song Wei , Li Jing , Liang Xiao , Chen Chen , Wang Shuai , Yang Beimeng , Chen Lei , Zhang Xu , Song Jinjing , Dong Yujie , Chen Shiqing , He Lin , Xie Qingguo , Chen Xiaoping , Li Weidong 
Published: September 2016

AbstractThere is an increasing risk of mental disorders, such as acute stress disorder (ASD), post-traumatic stress disorder (PTSD) and depression among survivors who were trapped in rubble during earthquake. Such long-term impaction of a single acute restraint stress has not been extensively explored. In this study, we subjected mice to 24-hour-restraint to simulate the trapping episode, and investigated the acute (2 days after the restraint) and long-term (35 days after the restraint) impacts. Surprisingly, we found that the mice displayed depression-like behaviors, decreased glucose uptake in brain and reduced adult hippocampal neurogenesis 35 days after the restraint. Differential expression profiling based on microarrays suggested that genes and pathways related to depression and other mental disorders were differentially expressed in both PFC and hippocampus. Furthermore, the depression-like phenotypes induced by 24-hour-restraint could be reversed by fluoxetine, a type of antidepressant drug. These findings demonstrated that a single severe stressful event could produce long-term depressive-like phenotypes. Moreover, the 24-hour-restraint stress mice could also be used for further studies on mood disorders.
Complete Defluorination of Perfluorinated Compounds by Hydrated Electrons Generated from 3-Indole-acetic-acid in Organomodified Montmorillonite
Authors: Tian Haoting , Gao Juan , Li Hui , Boyd Stephen A. , Gu Cheng 
Published: September 2016

AbstractHere we describe a unique process that achieves complete defluorination and decomposition of perfluorinated compounds (PFCs) which comprise one of the most recalcitrant and widely distributed classes of toxic pollutant chemicals found in natural environments. Photogenerated hydrated electrons derived from 3-indole-acetic-acid within an organomodified clay induce the reductive defluorination of co-sorbed PFCs. The process proceeds to completion within a few hours under mild reaction conditions. The organomontmorillonite clay promotes the formation of highly reactive hydrated electrons by stabilizing indole radical cations formed upon photolysis, and prevents their deactivation by reaction with protons or oxygen. In the constrained interlayer regions of the clay, hydrated electrons and co-sorbed PFCs are brought in close proximity thereby increasing the probability of reaction. This novel green chemistry provides the basis for in situ and ex situ technologies to treat one of the most troublesome, recalcitrant and ubiquitous classes of environmental contaminants, i.e., PFCs, utilizing innocuous reagents, naturally occurring materials and mild reaction conditions.
Computational imaging reveals mitochondrial morphology as a biomarker of cancer phenotype and drug response
Authors: Giedt Randy J. , Fumene Feruglio Paolo , Pathania Divya , Yang Katherine S. , Kilcoyne Aoife , Vinegoni Claudio , Mitchison Timothy J. , Weissleder Ralph 
Published: September 2016

AbstractMitochondria, which are essential organelles in resting and replicating cells, can vary in number, mass and shape. Past research has primarily focused on short-term molecular mechanisms underlying fission/fusion. Less is known about longer-term mitochondrial behavior such as the overall makeup of cell populations’ morphological patterns and whether these patterns can be used as biomarkers of drug response in human cells. We developed an image-based analytical technique to phenotype mitochondrial morphology in different cancers, including cancer cell lines and patient-derived cancer cells. We demonstrate that (i) cancer cells of different origins, including patient-derived xenografts, express highly diverse mitochondrial phenotypes; (ii) a given phenotype is characteristic of a cell population and fairly constant over time; (iii) mitochondrial patterns correlate with cell metabolic measurements and (iv) therapeutic interventions can alter mitochondrial phenotypes in drug-sensitive cancers as measured in pre- versus post-treatment fine needle aspirates in mice. These observations shed light on the role of mitochondrial dynamics in the biology and drug response of cancer cells. On the basis of these findings, we propose that image-based mitochondrial phenotyping can provide biomarkers for assessing cancer phenotype and drug response.
Development of a Cell-penetrating Peptide that Exhibits Responsive Changes in its Secondary Structure in the Cellular Environment
Authors: Yamashita Hiroko , Kato Takuma , Oba Makoto , Misawa Takashi , Hattori Takayuki , Ohoka Nobumichi , Tanaka Masakazu , Naito Mikihiko , Kurihara Masaaki , Demizu Yosuke 
Published: September 2016

AbstractCell-penetrating peptides (CPP) are received a lot of attention as an intracellular delivery tool for hydrophilic molecules such as drugs, proteins, and DNAs. We designed and synthesized nona-arginine analogues 1–5 [FAM-β-Ala-(l-Arg-l-Arg-l-Pro)3-(Gly)3-NH2 (1), FAM-β-Ala-(l-Arg-l-Arg-l-ProNH2)3-(Gly)3-NH2 (2), FAM-β-Ala-(l-Arg-l-Arg-l-ProGu)3-(Gly)3-NH2 (3), FAM-β-Ala-(l-Arg)2-(l-ProGu)2-(l-Arg)4-l-ProGu-(Gly)3-NH2 (4), and FAM-β-Ala-(l-Arg)6-(l-ProGu)3-(Gly)3-NH2 (5)] containing l-proline (l-Pro) or cationic proline derivatives (l-ProNH2 and l-ProGu), and investigated their cell-penetrating abilities. Interestingly, only peptide 3 having the side-chain guanidinyl l-ProGu exhibited a secondary structural change in cellular environment. Specifically, peptide 3 formed a random structure in hydrophilic conditions, whereas it formed a helical structure under amphipathic conditions. Furthermore, during cellular permeability tests, peptide 3 demonstrated greater cell-penetrating activity than other peptides and effectively transported plasmid DNA into HeLa cells. Thus, l-ProGu-containing peptide 3 may be a useful candidate as a gene delivery carrier.
Different strategies of metabolic regulation in cyanobacteria: from transcriptional to biochemical control
Authors: Jablonsky Jiri , Papacek Stepan , Hagemann Martin 
Published: September 2016

AbstractCyanobacteria Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 show similar changes in the metabolic response to changed CO2 conditions but exhibit significant differences at the transcriptomic level. This study employs a systems biology approach to investigate the difference in metabolic regulation of Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803. Presented multi-level kinetic model for Synechocystis sp. PCC 6803 is a new approach integrating and analysing metabolomic, transcriptomic and fluxomics data obtained under high and ambient CO2 levels. Modelling analysis revealed that higher number of different isozymes in Synechocystis 6803 improves homeostatic stability of several metabolites, especially 3PGA by 275%, against changes in gene expression, compared to Synechococcus sp. PCC 7942. Furthermore, both cyanobacteria have the same amount of phosphoglycerate mutases but Synechocystis 6803 exhibits only ~20% differences in their mRNA levels after shifts from high to ambient CO2 level, in comparison to ~500% differences in the case of Synechococcus sp. PCC 7942. These and other data imply that the biochemical control dominates over transcriptional regulation in Synechocystis 6803 to acclimate central carbon metabolism in the environment of variable inorganic carbon availability without extra cost carried by large changes in the proteome.
Microvesicles from brain-extract—treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke
Authors: Lee Ji Yong , Kim Eiru , Choi Seong-Mi , Kim Dong-Wook , Kim Kwang Pyo , Lee Insuk , Kim Han-Soo 
Published: September 2016

AbstractTransplantation of mesenchymal stem cells (MSCs) was reported to improve functional outcomes in a rat model of ischemic stroke, and subsequent studies suggest that MSC-derived microvesicles (MVs) can replace the beneficial effects of MSCs. Here, we evaluated three different MSC-derived MVs, including MVs from untreated MSCs (MSC-MVs), MVs from MSCs treated with normal rat brain extract (NBE-MSC-MVs), and MVs from MSCs treated with stroke-injured rat brain extract (SBE-MSC-MVs), and tested their effects on ischemic brain injury induced by permanent middle cerebral artery occlusion (pMCAO) in rats. NBE-MSC-MVs and SBE-MSC-MVs had significantly greater efficacy than MSC-MVs for ameliorating ischemic brain injury with improved functional recovery. We found similar profiles of key signalling proteins in NBE-MSC-MVs and SBE-MSC-MVs, which account for their similar therapeutic efficacies. Immunohistochemical analyses suggest that brain-extract—treated MSC-MVs reduce inflammation, enhance angiogenesis, and increase endogenous neurogenesis in the rat brain. We performed mass spectrometry proteomic analyses and found that the total proteomes of brain-extract—treated MSC-MVs are highly enriched for known vesicular proteins. Notably, MSC-MV proteins upregulated by brain extracts tend to be modular for tissue repair pathways. We suggest that MSC-MV proteins stimulated by the brain microenvironment are paracrine effectors that enhance MSC therapy for stroke injury.
Tracing the Attention of Moving Citizens
Authors: Wu Lingfei , Wang Cheng-Jun 
Published: September 2016

AbstractWith the widespread use of mobile computing devices in contemporary society, our trajectories in the physical space and virtual world are increasingly closely connected. Using the anonymous smartphone data of 1 × 105 users in a major city of China, we study the interplay between online and offline human behaviors by constructing the mobility network (offline) and the attention network (online). Using the network renormalization technique, we find that they belong to two different classes: the mobility network is small-world, whereas the attention network is fractal. We then divide the city into different areas based on the features of the mobility network discovered under renormalization. Interestingly, this spatial division manifests the location-based online behaviors, for example shopping, dating, and taxi-requesting. Finally, we offer a geometric network model to help us understand the relationship between small-world and fractal networks.
Methotrexate is not associated with increased liver cirrhosis in a population-based cohort of rheumatoid arthritis patients with chronic hepatitis C
Authors: Tang Kuo-Tung , Chen Yi-Hsing , Lin Ching-Heng , Chen Der-Yuan 
Published: September 2016

AbstractA few studies have shown that methotrexate (MTX) use exacerbates liver fibrosis and even leads to liver cirrhosis in rheumatoid arthritis (RA) patients, although the risk is low compared to psoriatics. We therefore conducted a population-based cohort study to investigate the impact of long-term MTX use on the risk of chronic hepatitis C (CHC)-related cirrhosis among RA patients. We analyzed data from the National Health Insurance Research Database in Taiwan and identified 450 incident cases of RA among CHC patients (255 MTX users and 195 MTX non-users) from January 1, 1998 to December 31, 2007. After a median follow-up of more than 5 years since the diagnosis of CHC, a total of 55 (12%) patients developed liver cirrhosis. We did not find an increased risk of liver cirrhosis among CHC patients with long-term MTX use for RA. Furthermore, there was no occurrence of liver cirrhosis among the 43 MTX users with a cumulative dose ≧3 grams after 108 months of treatment. In conclusion, our data showed that long-term MTX use is not associated with an increased risk for liver cirrhosis among RA patients with CHC. However, these results should be interpreted with caution due to potential bias in the cohort.