bluuebunny/crossref_metadata_2025_split huggingface dataset:
Megacity pumping and preferential flow threaten groundwater quality
Authors: Khan Mahfuzur R. , Koneshloo Mohammad , Knappett Peter S. K. , Ahmed Kazi M. , Bostick Benjamin C. , Mailloux Brian J. , Mozumder Rajib H. , Zahid Anwar , Harvey Charles F. , van Geen Alexander , Michael Holly A. 
Published: September 2016

AbstractMany of the world’s megacities depend on groundwater from geologically complex aquifers that are over-exploited and threatened by contamination. Here, using the example of Dhaka, Bangladesh, we illustrate how interactions between aquifer heterogeneity and groundwater exploitation jeopardize groundwater resources regionally. Groundwater pumping in Dhaka has caused large-scale drawdown that extends into outlying areas where arsenic-contaminated shallow groundwater is pervasive and has potential to migrate downward. We evaluate the vulnerability of deep, low-arsenic groundwater with groundwater models that incorporate geostatistical simulations of aquifer heterogeneity. Simulations show that preferential flow through stratigraphy typical of fluvio-deltaic aquifers could contaminate deep (>150 m) groundwater within a decade, nearly a century faster than predicted through homogeneous models calibrated to the same data. The most critical fast flowpaths cannot be predicted by simplified models or identified by standard measurements. Such complex vulnerability beyond city limits could become a limiting factor for megacity groundwater supplies in aquifers worldwide.
CARD9 negatively regulates NLRP3-induced IL-1β production on Salmonella infection of macrophages
Authors: Pereira Milton , Tourlomousis Panagiotis , Wright John , P. Monie Tom , Bryant Clare E. 
Published: September 2016

AbstractInterleukin-1β (IL-1β) is a proinflammatory cytokine required for host control of bacterial infections, and its production must be tightly regulated to prevent excessive inflammation. Here we show that caspase recruitment domain-containing protein 9 (CARD9), a protein associated with induction of proinflammatory cytokines by fungi, has a negative role on IL-1β production during bacterial infection. Specifically, in response to activation of the nucleotide oligomerization domain receptor pyrin-domain containing protein 3 (NLRP3) by Salmonella infection, CARD9 negatively regulates IL-1β by fine-tuning pro-IL-1β expression, spleen tyrosine kinase (SYK)-mediated NLRP3 activation and repressing inflammasome-associated caspase-8 activity. CARD9 is suppressed during Salmonella enterica serovar Typhimurium infection, facilitating increased IL-1β production. CARD9 is, therefore, a central signalling hub that coordinates a pathogen-specific host inflammatory response.
An electrical analogy to Mie scattering
Authors: Caridad José M. , Connaughton Stephen , Ott Christian , Weber Heiko B. , Krstić Vojislav 
Published: September 2016

AbstractMie scattering is an optical phenomenon that appears when electromagnetic waves, in particular light, are elastically scattered at a spherical or cylindrical object. A transfer of this phenomenon onto electron states in ballistic graphene has been proposed theoretically, assuming a well-defined incident wave scattered by a perfectly cylindrical nanometer scaled potential, but experimental fingerprints are lacking. We present an experimental demonstration of an electrical analogue to Mie scattering by using graphene as a conductor, and circular potentials arranged in a square two-dimensional array. The tabletop experiment is carried out under seemingly unfavourable conditions of diffusive transport at room-temperature. Nonetheless, when a canted arrangement of the array with respect to the incident current is chosen, cascaded Mie scattering results robustly in a transverse voltage. Its response on electrostatic gating and variation of potentials convincingly underscores Mie scattering as underlying mechanism. The findings presented here encourage the design of functional electronic metamaterials.
Population and hierarchy of active species in gold iron oxide catalysts for carbon monoxide oxidation
Authors: He Qian , Freakley Simon J. , Edwards Jennifer K. , Carley Albert F. , Borisevich Albina Y. , Mineo Yuki , Haruta Masatake , Hutchings Graham J. , Kiely Christopher J. 
Published: September 2016

AbstractThe identity of active species in supported gold catalysts for low temperature carbon monoxide oxidation remains an unsettled debate. With large amounts of experimental evidence supporting theories of either gold nanoparticles or sub-nm gold species being active, it was recently proposed that a size-dependent activity hierarchy should exist. Here we study the diverging catalytic behaviours after heat treatment of Au/FeOx materials prepared via co-precipitation and deposition precipitation methods. After ruling out any support effects, the gold particle size distributions in different catalysts are quantitatively studied using aberration corrected scanning transmission electron microscopy (STEM). A counting protocol is developed to reveal the true particle size distribution from HAADF-STEM images, which reliably includes all the gold species present. Correlation of the populations of the various gold species present with catalysis results demonstrate that a size-dependent activity hierarchy must exist in the Au/FeOx catalyst.
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration
Authors: Smid Marcel , Rodríguez-González F. Germán , Sieuwerts Anieta M. , Salgado Roberto , Prager-Van der Smissen Wendy J. C. , Vlugt-Daane Michelle van der , van Galen Anne , Nik-Zainal Serena , Staaf Johan , Brinkman Arie B. , van de Vijver Marc J. , Richardson Andrea L. , Fatima Aquila , Berentsen Kim , Butler Adam , Martin Sancha , Davies Helen R. , Debets Reno , Gelder Marion E. Meijer-Van , van Deurzen Carolien H. M. , MacGrogan Gaëtan , Van den Eynden Gert G. G. M. , Purdie Colin , Thompson Alastair M. , Caldas Carlos , Span Paul N. , Simpson Peter T. , Lakhani Sunil R. , Van Laere Steven , Desmedt Christine , Ringnér Markus , Tommasi Stefania , Eyford Jorunn , Broeks Annegien , Vincent-Salomon Anne , Futreal P. Andrew , Knappskog Stian , King Tari , Thomas Gilles , Viari Alain , Langerød Anita , Børresen-Dale Anne-Lise , Birney Ewan , Stunnenberg Hendrik G. , Stratton Mike , Foekens John A. , Martens John W. M. 
Published: September 2016

AbstractA recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example,TP53, PIK3CA, PTEN, CCND1andCDH1. We find thatCCND3expression levels do not correlate with amplification, while increasedGATA3expression in mutantGATA3cancers suggestsGATA3is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.
A cholinergic-sympathetic pathway primes immunity in hypertension and mediates brain-to-spleen communication
Authors: Carnevale Daniela , Perrotta Marialuisa , Pallante Fabio , Fardella Valentina , Iacobucci Roberta , Fardella Stefania , Carnevale Lorenzo , Carnevale Raimondo , De Lucia Massimiliano , Cifelli Giuseppe , Lembo Giuseppe 
Published: September 2016

AbstractThe crucial role of the immune system in hypertension is now widely recognized. We previously reported that hypertensive challenges couple the nervous drive with immune system activation, but the physiological and molecular mechanisms of this connection are unknown. Here, we show that hypertensive challenges activate splenic sympathetic nerve discharge to prime immune response. More specifically, a vagus-splenic nerve drive, mediated by nicotinic cholinergic receptors, links the brain and spleen. The sympathetic discharge induced by hypertensive stimuli was absent in both coeliac vagotomized mice and in mice lacking α7nAChR, a receptor typically expressed by peripheral ganglionic neurons. This cholinergic-sympathetic pathway is necessary for T cell activation and egression on hypertensive challenges. In addition, we show that selectively thermoablating the splenic nerve prevents T cell egression and protects against hypertension. This novel experimental procedure for selective splenic denervation suggests new clinical strategies for resistant hypertension.
Control of cortex development by ULK4, a rare risk gene for mental disorders including schizophrenia
Authors: Lang Bing , Zhang Lei , Jiang Guanyu , Hu Ling , Lan Wei , Zhao Lei , Hunter Irene , Pruski Michal , Song Ning-Ning , Huang Ying , Zhang Ling , St Clair David , McCaig Colin D. , Ding Yu-Qiang 
Published: September 2016

AbstractSchizophrenia is a debilitating familial neuropsychiatric disorder which affects 1% of people worldwide. Although the heritability for schizophrenia approaches 80% only a small proportion of the overall genetic risk has been accounted for and to date only a limited number of genetic loci have been definitively implicated. We have identified recently through genetic and in vitro functional studies, a novel serine/threonine kinase gene, unc-51-like kinase 4 (ULK4), as a rare risk factor for major mental disorders including schizophrenia. Now using the approach of in utero gene transfer we have discovered that Ulk4 plays a key modulatory role in corticogenesis. Knockdown of Ulk4 leads to significantly decreased cell proliferation in germinal zones and profound deficits in radial migration and neurite ramification. These abnormalities can be reversed successfully by Ulk4 gene supplementation. Ulk4 also regulated acetylation of α-tubulin, an important post-translational modification of microtubules. We conclude that Ulk4 plays an essential role in normal brain development and when defective, the risk of neurodevelopmental disorders such as schizophrenia is increased.
Combination treatment with decitabine and ionizing radiation enhances tumor cells susceptibility of T cells
Authors: Son Cheol-Hun , Lee Hong-Rae , Koh Eun-Kyoung , Shin Dong-Yeok , Bae Jae-Ho , Yang Kwangmo , Park You-Soo 
Published: September 2016

AbstractDecitabine has been found to have anti-metabolic and anti-tumor activities in various tumor cells. Recently, the use of decitabine in combination with other conventional therapies reportedly resulted in improved anti-tumor activity against various tumors. Ionizing radiation (IR) is widely used as a cancer treatment. Decitabine and IR improve immunogenicity and susceptibility of tumor cells to immune cells by up-regulating the expression of various molecules such as major histocompatibility complex (MHC) class I; natural-killer group 2, member D (NKG2D) ligands; and co-stimulatory molecules. However, the effects of combining decitabine and IR therapies are largely unknown. Our results indicate that decitabine or IR treatment upregulates MHC class I, along with various co-stimulatory molecules in target tumor cells. Furthermore, decitabine and IR combination treatment further upregulates MHC class I, along with the co-stimulatory molecules, when compared to the effect of each treatment alone. Importantly, decitabine treatment further enhanced T cell-mediated cytotoxicity and release of IFN- γ against target tumor cells which is induced by IR. Interestingly, decitabine did not affect NKG2D ligand expression or NK cell-mediated cytotoxicity in target tumor cells. These observations suggest that decitabine may be used as a useful immunomodulator to sensitize tumor cells in combination with other tumor therapies.
Efficacy and safety of TNF-α inhibitors for active ankylosing spondylitis patients: Multiple treatment comparisons in a network meta-analysis
Authors: Liu Wei , Wu Yuan-hao , Zhang Lei , Liu Xiao-ya , Bin Xue  , Bin Liu  , Wang Yi , Ji Yang 
Published: September 2016

AbstractAnkylosing spondylitis (AS) is an inflammatory rheumatic disease with impact on axial skeleton, peripheral joints and enthuses, and it may result in severe disabilities of those parts. Tumor necrosis factor-α (TNF-α) inhibitors are considered as an effective treatment for patients with active AS. In this study, we conducted a network meta-analysis to compare the clinical outcomes of active AS patients treated with TNF-α inhibitors. Randomized controlled trials (RCTs) evaluating the efficacy and safety of TNF-α inhibitors were retrieved in literature search and selected for meta-analysis. Changes in ASAS20 response, ASAS40 response and BASDAI 50% response were regarded as efficacy outcomes; serious adverse events (SAE) and all cause withdrawals were regarded as safety outcomes. Both traditional pairwise meta-analysis and network meta-analysis were performed. The results showed that adalimumab and infliximab had better clinical outcomes. Infliximab consistently appeared to be the most effective TNF-α inhibitors with a high risk of adverse events for patients with active AS; meanwhile, adalimumab ranked highest with respect to adverse effects with efficacy secondary to infliximab. As a result, we were unable to conclude the optimal TNF-α inhibitor and this issue should be solved by future researchers.
Self-Assembly of Amphiphilic Block Copolypeptoids – Micelles, Worms and Polymersomes
Authors: Fetsch Corinna , Gaitzsch Jens , Messager Lea , Battaglia Giuseppe , Luxenhofer Robert 
Published: September 2016

AbstractPolypeptoids are an old but recently rediscovered polymer class with interesting synthetic, physico-chemical and biological characteristics. Here, we introduce new aromatic monomers, N-benzyl glycine N-carboxyanhydride and N-phenethyl glycine N-carboxyanhydride and their block copolymers with the hydrophilic polysarcosine. We compare their self-assembly in water and aqueous buffer with the self-assembly of amphiphilic block copolypeptoids with aliphatic side chains. The aggregates in water were investigated by dynamic light scattering and electron microscopy. We found a variety of morphologies, which were influenced by the polymer structure as well as by the preparation method. Overall, we found polymersomes, worm-like micelles and oligo-lamellar morphologies as well as some less defined aggregates of interconnected worms and vesicles. Such, this contribution may serve as a starting point for a more detailed investigation of the self-assembly behavior of the rich class of polypeptoids and for a better understanding between the differences in the aggregation behavior of non-uniform polypeptoids and uniform peptoids.
Textile Organic Electrochemical Transistors as a Platform for Wearable Biosensors
Authors: Gualandi I. , Marzocchi M. , Achilli A. , Cavedale D. , Bonfiglio A. , Fraboni B. 
Published: September 2016

AbstractThe development of wearable chemical sensors is receiving a great deal of attention in view of non-invasive and continuous monitoring of physiological parameters in healthcare applications. This paper describes the development of a fully textile, wearable chemical sensor based on an organic electrochemical transistor (OECT) entirely made of conductive polymer (PEDOT:PSS). The active polymer patterns are deposited into the fabric by screen printing processes, thus allowing the device to actually “disappear” into it. We demonstrate the reliability of the proposed textile OECTs as a platform for developing chemical sensors capable to detect in real-time various redox active molecules (adrenaline, dopamine and ascorbic acid), by assessing their performance in two different experimental contexts: i) ideal operation conditions (i.e. totally dipped in an electrolyte solution); ii) real-life operation conditions (i.e. by sequentially adding few drops of electrolyte solution onto only one side of the textile sensor). The OECTs response has also been measured in artificial sweat, assessing how these sensors can be reliably used for the detection of biomarkers in body fluids. Finally, the very low operating potentials (<1 V) and absorbed power (~10−4W) make the here described textile OECTs very appealing for portable and wearable applications.
Whole exome sequencing identified novel CRB1 mutations in Chinese and Indian populations with autosomal recessive retinitis pigmentosa
Authors: Yang Yin , Yang Yeming , Huang Lulin , Zhai Yaru , Li Jie , Jiang Zhilin , Gong Bo , Fang Hao , Kim Ramasamy , Yang Zhenglin , Sundaresan Periasamy , Zhu Xianjun , Zhou Yu 
Published: September 2016

AbstractRetinitis pigmentosa (RP) is a leading cause of inherited blindness characterized by progressive degeneration of the retinal photoreceptor cells. This study aims to identify genetic mutations in a Chinese family RP-2236, an Indian family RP-IC-90 and 100 sporadic Indian individuals with autosomal recessive RP (arRP). Whole exome sequencing was performed on the index patients of RP-2236, RP-IC-90 and all of the 100 sporadic Indian patients. Direct Sanger sequencing was used to validate the mutations identified. Four novel mutations and one reported mutation in the crumbs homolog 1 (CRB1) gene, which has been known to cause severe retinal dystrophies, were identified. A novel homozygous splicing mutation c.2129-1G>C was found in the three patients In family RP-2236. A homozygous point mutation p.R664C was found in RP-IC-90. A novel homozygous mutation p.G1310C was identified in patient I-44, while novel compound heterozygous mutations p.N629D and p.A593T were found in patient I-7. All mutations described above were not present in the 1000 normal controls. In conclusion, we identified four novel mutations in CRB1 in a cohort of RP patients from the Chinese and Indian populations. Our data enlarges the CRB1 mutation spectrums and may provide new target loci for RP diagnose and treatment.
Trackways Produced by Lungfish During Terrestrial Locomotion
Authors: Falkingham Peter L. , Horner Angela M. 
Published: September 2016

AbstractSome primarily aquatic vertebrates make brief forays onto land, creating traces as they do. A lack of studies on aquatic trackmakers raises the possibility that such traces may be ignored or misidentified in the fossil record. Several terrestrial Actinopterygian and Sarcopterygian species have previously been proposed as possible models for ancestral tetrapod locomotion, despite extant fishes being quite distinct from Devonian fishes, both morphologically and phylogenetically. Although locomotion has been well-studied in some of these taxa, trackway production has not. We recorded terrestrial locomotion of a 35 cm African lungfish (Protopterus annectens; Dipnoi: Sarcopterygii) on compliant sediment. Terrestrial movement in the lungfish is accomplished by planting the head and then pivoting the trunk. Impressions are formed where the head impacts the substrate, while the body and fins produce few traces. The head leaves a series of alternating left-right impressions, where each impact can appear as two separate semi-circular impressions created by the upper and lower jaws, bearing some similarity to fossil traces interpreted as footprints. Further studies of trackways of extant terrestrial fishes are necessary to understand the behavioural repertoire that may be represented in the fossil track record.
Gastrectomy is Associated with an Increased Risk of Pyogenic Liver Abscess: A 13-Year Nationwide Cohort Study
Authors: Tsai Ming-Shian , Lin Cheng-Li , Jeng Long-Bin 
Published: September 2016

AbstractWhether patients who have undergone gastrectomy are at a high risk of developing pyogenic liver abscess (PLA) remains debatable. From the inpatient claims records of Taiwan’s National Health Insurance Research Database, we identified 33 834 patients with a history of 2000–2010 and135 336 controls without a history of gastrectomy. The 2cohorts were matched by age, sex, and admission year and followed-up until the end of 2011 for estimating the risk of PLA. Overall, the incidence of PLA was 3.5-fold higher in the gastrectomy cohort than in the control cohort (21.6 vs 5.76 per 10 000 person-y). The adjusted hazard ratio (aHR) for the gastrectomy cohort obtained using the multivariate Cox proportional hazards regression model was 3.08 (95% confidence interval [CI] = 2.60–3.64). An elevated post gastrectomy PLA risk was observed in both men and women. Age-specific data revealed that the aHR for the gastrectomy cohort, compared with the control cohort, was the highest in patients younger than 50 years (aHR = 5.16, 95% CI = 2.96–9.01). An addition analysis showed that the gastrectomy cohort exhibited an elevated PLA risk regardless of whether the patients underwent total or partial gastrectomy. Patients with a history of gastrectomy exhibit a high risk of PLA.
Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients
Authors: Hou Dongni , Ying Tianlei , Wang Lili , Chen Cuicui , Lu Shuihua , Wang Qin , Seeley Eric , Xu Jianqing , Xi Xiuhong , Li Tao , Liu Jie , Tang Xinjun , Zhang Zhiyong , Zhou Jian , Bai Chunxue , Wang Chunlin , Byrne-Steele Miranda , Qu Jieming , Han Jian , Song Yuanlin 
Published: September 2016

AbstractSpecific changes in immune repertoires at genetic level responding to the lethal H7N9 virus are still poorly understood. We performed deep sequencing on the T and B cells from patients recently infected with H7N9 to explore the correlation between clinical outcomes and immune repertoire alterations. T and B cell repertoires display highly dynamic yet distinct clonotype alterations. During infection, T cell beta chain repertoire continues to contract while the diversity of immunoglobulin heavy chain repertoire recovers. Patient recovery is correlated to the diversity of T cell and B cell repertoires in different ways – higher B cell diversity and lower T cell diversity are found in survivors. The sequences clonally related to known antibodies with binding affinity to H7 hemagglutinin could be identified from survivors. These findings suggest that utilizing deep sequencing may improve prognostication during influenza infection and could help in development of antibody discovery methodologies for the treatment of virus infection.
Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light
Authors: Becker Anja , Klapczynski Anna , Kuch Natalia , Arpino Fabiola , Simon-Keller Katja , De La Torre Carolina , Sticht Carsten , van Abeelen Frank A. , Oversluizen Gerrit , Gretz Norbert 
Published: September 2016

AbstractPhotobiomodulation (PBM) with blue light induces a biphasic dose response curve in proliferation of immortalized human keratinocytes (HaCaT), with a maximum anti-proliferative effect reached with 30min (41.4 J/cm2). The aim of this study was to test the photobiomodulatory effect of 41.4 J/cm2 blue light irradiation on ROS production, apoptosis and gene expression at different time points after irradiation of HaCaT cells in vitro and assess its safety. ROS concentration was increased 30 min after irradiation. However, already 1 h after irradiation, cells were able to reduce ROS and balance the concentration to a normal level. The sudden increase in ROS did not damage the cells, which was demonstrated with FACS analysis where HaCaT cells did not show any sign of apoptosis after blue light irradiation. Furthermore, a time course could be seen in gene expression analysis after blue light, with an early response of stimulated genes already 1 h after blue light irradiation, leading to the discovery of the aryl hydrocarbon receptor as possible target for blue light irradiation.