bluuebunny/crossref_metadata_2025_split huggingface dataset:
Projection of American dustiness in the late 21st century due to climate change
Authors: Pu Bing , Ginoux Paul 
Published: July 2017

AbstractClimate models project rising drought risks over the southwestern and central U.S. in the twenty-first century due to increasing greenhouse gases. The projected drier regions largely overlay the major dust sources in the United States. However, whether dust activity in U.S. will increase in the future is not clear, due to the large uncertainty in dust modeling. This study found that changes of dust activity in the U.S. in the recent decade are largely associated with the variations of precipitation, soil bareness, and surface winds speed. Using multi-model output under the Representative Concentration Pathways 8.5 scenario, we project that climate change will increase dust activity in the southern Great Plains from spring to fall in the late half of the twenty-first century – largely due to reduced precipitation, enhanced land surface bareness, and increased surface wind speed. Over the northern Great Plains, less dusty days are expected in spring due to increased precipitation and reduced bareness. Given the large negative economic and societal consequences of severe dust storms, this study complements the multi-model projection on future dust variations and may help improve risk management and resource planning.
Hyper-Stain Inspector: A Framework for Robust Registration and Localised Co-Expression Analysis of Multiple Whole-Slide Images of Serial Histology Sections
Authors: Trahearn Nicholas , Epstein David , Cree Ian , Snead David , Rajpoot Nasir 
Published: July 2017

AbstractIn this paper, we present a fast method for registration of multiple large, digitised whole-slide images (WSIs) of serial histology sections. Through cross-slide WSI registration, it becomes possible to select and analyse a common visual field across images of several serial section stained with different protein markers. It is, therefore, a critical first step for any downstream co-localised cross-slide analysis. The proposed registration method uses a two-stage approach, first estimating a fast initial alignment using the tissue sections’ external boundaries, followed by an efficient refinement process guided by key biological structures within the visual field. We show that this method is able to produce a high quality alignment in a variety of circumstances, and demonstrate that the refinement is able to quantitatively improve registration quality. In addition, we provide a case study that demonstrates how the proposed method for cross-slide WSI registration could be used as part of a specific co-expression analysis framework.
Proton Pump Inhibitors and the Risk for Fracture at Specific Sites: Data Mining of the FDA Adverse Event Reporting System
Authors: Wang Liwei , Li Mei , Cao Yuying , Han Zhengqi , Wang Xueju , Atkinson Elizabeth J. , Liu Hongfang , Amin Shreyasee 
Published: July 2017

AbstractProton pump inhibitors (PPIs) are widely used to treat gastric acid-related disorders. Concerns have been raised about potential fracture risk, especially at the hip, spine and wrist. However, fracture risk at other bone sites has not been as well studied. We investigated the association between PPIs and specific fracture sites using an aggregated knowledge-enhanced database, the Food and Drug Administration Adverse Event Reporting System Data Mining Set (AERS-DM). Proportional reporting ratio (PRR) was used to detect statistically significant associations (signals) between PPIs and fractures. We analyzed both high level terms (HLT) and preferred terms (PT) for fracture sites, defined by MedDRA (Medical Dictionary for Regulatory Activities). Of PPI users reporting fractures, the mean age was 65.3 years and the female to male ratio was 3.4:1. Results revealed signals at multiple HLT and PT fracture sites, consistent for both sexes. These included fracture sites with predominant trabecular bone, not previously reported as being associated with PPIs, such as ‘rib fractures’, where signals were detected for overall PPIs as well as for each of 5 generic ingredients (insufficient data for dexlansoprazole). Based on data mining from AERS-DM, PPI use appears to be associated with an increased risk for fractures at multiple sites.
Evolution of the Pseudomonas aeruginosa mutational resistome in an international Cystic Fibrosis clone
Authors: López-Causapé Carla , Sommer Lea Mette , Cabot Gabriel , Rubio Rosa , Ocampo-Sosa Alain A. , Johansen Helle Krogh , Figuerola Joan , Cantón Rafael , Kidd Timothy J. , Molin Soeren , Oliver Antonio 
Published: July 2017

AbstractEmergence of epidemic clones and antibiotic resistance development compromises the management of Pseudomonas aeruginosa cystic fibrosis (CF) chronic respiratory infections. Whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, WGS mutator genotypes (mutome) and resistome of a widespread clone (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. The coexistence of two divergent CC274 clonal lineages was revealed, but without evident geographical barrier; phylogenetic reconstructions and mutational resistome demonstrated the interpatient transmission of mutators. The extraordinary capacity of P. aeruginosa to develop resistance was evidenced by the emergence of mutations in >100 genes related to antibiotic resistance during the evolution of CC274, catalyzed by mutator phenotypes. While the presence of classical mutational resistance mechanisms was confirmed and correlated with resistance phenotypes, results also showed a major role of unexpected mutations. Among them, PBP3 mutations, shaping up β-lactam resistance, were noteworthy. A high selective pressure for mexZ mutations was evidenced, but we showed for the first time that high-level aminoglycoside resistance in CF is likely driven by mutations in fusA1/fusA2, coding for elongation factor G. Altogether, our results provide valuable information for understanding the evolution of the mutational resistome of CF P. aeruginosa.
Association Of Plasma And Urinary Mutant DNA With Clinical Outcomes In Muscle Invasive Bladder Cancer
Authors: Patel K. M. , van der Vos K. E. , Smith C. G. , Mouliere F. , Tsui D. , Morris J. , Chandrananda D. , Marass F. , van den Broek D. , Neal D. E. , Gnanapragasam V. J. , Forshew T. , van Rhijn B. W. , Massie C. E. , Rosenfeld N. , van der Heijden M. S. 
Published: July 2017

AbstractMuscle Invasive Bladder Cancer (MIBC) has a poor prognosis. Whilst patients can achieve a 6% improvement in overall survival with Neo-Adjuvant Chemotherapy (NAC), many do not respond. Body fluid mutant DNA (mutDNA) may allow non-invasive identification of treatment failure. We collected 248 liquid biopsy samples including plasma, cell pellet (UCP) and supernatant (USN) from spun urine, from 17 patients undergoing NAC. We assessed single nucleotide variants and copy number alterations in mutDNA using Tagged-Amplicon- and shallow Whole Genome- Sequencing. MutDNA was detected in 35.3%, 47.1% and 52.9% of pre-NAC plasma, UCP and USN samples respectively, and urine samples contained higher levels of mutDNA (p = <0.001). Longitudinal mutDNA demonstrated tumour evolution under the selective pressure of NAC e.g. in one case, urine analysis tracked two distinct clones with contrasting treatment sensitivity. Of note, persistence of mutDNA detection during NAC predicted disease recurrence (p = 0.003), emphasising its potential as an early biomarker for chemotherapy response.
Phonon Surface Scattering and Thermal Energy Distribution in Superlattices
Authors: Kothari Kartik , Maldovan Martin 
Published: July 2017

AbstractThermal transport at small length scales has attracted significant attention in recent years and various experimental and theoretical methods have been developed to establish the reduced thermal conductivity. The fundamental understanding of how phonons move and the physical mechanisms behind nanoscale thermal transport, however, remains poorly understood. Here we move beyond thermal conductivity calculations and provide a rigorous and comprehensive physical description of thermal phonon transport in superlattices by solving the Boltzmann transport equation and using the Beckman-Kirchhoff surface scattering theory with shadowing to precisely describe phonon-surface interactions. We show that thermal transport in superlattices can be divided in two different heat transport modes having different physical properties at small length scales: layer-restricted and extended heat modes. We study how interface conditions, periodicity, and composition can be used to manipulate the distribution of thermal energy flow among such layer-restricted and extended heat modes. From predicted frequency and mean free path spectra of superlattices, we also investigate the existence of wave effects. The results and insights in this paper advance the fundamental understanding of heat transport in superlattices and the prospects of rationally designing thermal systems with tailored phonon transport properties.
Effects of Population Bottleneck and Balancing Selection on the Chinese Alligator Are Revealed by Locus-Specific Characterization of MHC Genes
Authors: Zhai Teng , Yang Hai-Qiong , Zhang Rui-Can , Fang Li-Ming , Zhong Guo-Heng , Fang Sheng-Guo 
Published: July 2017

AbstractChinese alligator (Alligator sinensis) is an endangered freshwater crocodilian endemic to China, which experienced a severe bottleneck about 30 years ago. In this study, we developed locus-specific primers to investigate the polymorphism of 3 major histocompatibility complex (MHC) loci in 3 Chinese alligator populations, in combination with 6 neutral microsatellite markers as a contrast. We found the genetic trace for the bottleneck effect on the endangered Chinese alligator: the low allelic diversity (2 alleles at each locus), the low nucleotide substitution rate (no more than 0.009) at all sites, the deviation from Hardy-Weinberg Equilibrium/heterozygote deficiency, and the significant Tajima’s D values, indicating the MHC class I and class II loci being at different stages of bottleneck. We also obtained 3 pieces of evidence for balancing selection on this severely bottlenecked reptile: an obvious excess of nonsynonymous substitutions over synonymous at the antigen-binding positions, the mean synonymous substitution rate of MHC exons significantly higher than mean nucleotide substitution rate of introns, and the differentiation coefficient FST of MHC loci significantly lower than that of microsatellite loci. Consequently, we emphasize that the Chinese alligator holds a pretty low adaptive ability and requires scientific conservation strategies to ensure the long-term population development.
Fungal infestation boosts fruit aroma and fruit removal by mammals and birds
Authors: Peris Josep E. , Rodríguez Ana , Peña Leandro , Fedriani José María 
Published: July 2017

AbstractFor four decades, an influential hypothesis has posited that competition for food resources between microbes and vertebrates selects for microbes to alter these resources in ways that make them unpalatable to vertebrates. We chose an understudied cross kingdom interaction to experimentally evaluate the effect of fruit infection by fungi on both vertebrate (mammals and birds) fruit preferences and on ecologically relevant fruit traits (volatile compounds, toughness, etc). Our well-replicated field experiments revealed that, in contrast to previous studies, frugivorous mammals and birds consistently preferred infested over intact fruits. This was concordant with the higher level of attractive volatiles (esters, ethanol) in infested fruits. This investigation suggests that vertebrate frugivores, fleshy-fruited plants, and microbes form a tripartite interaction in which each part could interact positively with the other two (e.g. both orange seeds and fungal spores are likely dispersed by mammals). Such a mutualistic view of these complex interactions is opposed to the generalized idea of competition between frugivorous vertebrates and microorganisms. Thus, this research provides a new perspective on the widely accepted plant evolutionary dilemma to make fruits attractive to mutualistic frugivores while unattractive to presumed antagonistic microbes that constrain seed dispersal.
The long non-coding RNA LOC441204 enhances cell growth in human glioma
Authors: Lin Tzu-Kang , Chang Chang-Nen , Tsai Cheng-Shian , Huang Yin-Cheng , Lu Yu-Jen , Chen Wei-Jan , Lin Yang-Hsiang , Chung I.-Hsiao , Lin Kwang-Huei 
Published: July 2017

AbstractGlioma is the most common and aggressive type of brain tumor. While long non-coding RNAs (lncRNAs) are clearly more abundant in human brain than protein-coding genes, the specific roles of lncRNAs and mechanisms underlying their dysregulation in glioma remain unclear. Here, we focused on lncRNAs that are differentially expressed in brain tumor and their potential biological functions. LOC441204, a novel non-coding RNA gene displaying high expression in clinical specimens of brain tumor and significant upregulation in glioma cell lines in microarray analyses, was selected for further study. Notably, knockdown of LOC441204 suppressed tumor cell proliferation in two glioma cell lines. Moreover, LOC441204-induced tumor cell growth was mediated the stabilization of β-catenin pathway. Briefly, LOC441204 bound to β-catenin preventing its degradation, resulting in downstream p21 repression and cdk4 activation to enhance glioma cell proliferation. Collectively, our findings indicate a pro-oncogenic role of LOC441204 in tumor cell growth through activation of the β-catenin/p21/cdk4 cascade to act as a potential diagnostic marker or therapeutic target in brain tumor.
Fiber cavities with integrated mode matching optics
Authors: Gulati Gurpreet Kaur , Takahashi Hiroki , Podoliak Nina , Horak Peter , Keller Matthias 
Published: July 2017

AbstractIn fiber based Fabry-Pérot Cavities (FFPCs), limited spatial mode matching between the cavity mode and input/output modes has been the main hindrance for many applications. We have demonstrated a versatile mode matching method for FFPCs. Our novel design employs an assembly of a graded-index and large core multimode fiber directly spliced to a single mode fiber. This all-fiber assembly transforms the propagating mode of the single mode fiber to match with the mode of a FFPC. As a result, we have measured a mode matching of 90% for a cavity length of ~400 μm. This is a significant improvement compared to conventional FFPCs coupled with just a single mode fiber, especially at long cavity lengths. Adjusting the parameters of the assembly, the fundamental cavity mode can be matched with the mode of almost any single mode fiber, making this approach highly versatile and integrable.
Experimental evidence reveals the UCP1 genotype changes the oxygen consumption attributed to non-shivering thermogenesis in humans
Authors: Nishimura Takayuki , Katsumura Takafumi , Motoi Midori , Oota Hiroki , Watanuki Shigeki 
Published: July 2017

AbstractHumans have spread out all over the world adapting to many different cold environments. Recent worldwide genome analyses and animal experiments have reported dozens of genes associated with cold adaptation. The uncoupling protein 1 (UCP1) gene enhances thermogenesis reaction in a physiological process by blocking ATP (adenosine triphosphate) synthesis on a mitochondrial membrane in brown adipose tissues. To our knowledge, no previous studies have shown an association between variants of the UCP1 gene and physiological phenotypes concerning non-shivering thermogenesis (NST) under the condition of low temperature in humans. We showed that the degree of NST for healthy subjects in an artificial climate chamber is significantly different among UCP1 genotypes. Defining the haplotypes covering the UCP1 region (39.4 kb), we found that the frequency of the haplotype with the highest NST was significantly correlated with latitudes and ambient temperature. Thus, the data in this study provide the first evidence that the UCP1 genotype alters the efficiency of NST in humans, and likely supports the hypothesis that the UCP1 gene has been related to cold adaptation in human evolutionary history.
Prostacyclin reverses platelet stress fibre formation causing platelet aggregate instability
Authors: Yusuf M. Z. , Raslan Z. , Atkinson L. , Aburima A. , Thomas S. G. , Naseem K. M. , Calaminus S. D. J. 
Published: July 2017

AbstractProstacyclin (PGI2) modulates platelet activation to regulate haemostasis. Evidence has emerged to suggest that thrombi are dynamic structures with distinct areas of differing platelet activation. It was hypothesised that PGI2 could reverse platelet spreading by actin cytoskeletal modulation, leading to reduced capability of platelet aggregates to withstand a high shear environment. Our data demonstrates that post-flow of PGI2 over activated and spread platelets on fibrinogen, identified a significant reduction in platelet surface area under high shear. Exploration of the molecular mechanisms underpinning this effect revealed that PGI2 reversed stress fibre formation in adherent platelets, reduced platelet spreading, whilst simultaneously promoting actin nodule formation. The effects of PGI2 on stress fibres were mimicked by the adenylyl cyclase activator forskolin and prevented by inhibitors of protein kinase A (PKA). Stress fibre formation is a RhoA dependent process and we found that treatment of adherent platelets with PGI2 caused inhibitory phosphorylation of RhoA, reduced RhoA GTP-loading and reversal of myosin light chain phosphorylation. Phospho-RhoA was localised in actin nodules with PKA type II and a number of other phosphorylated PKA substrates. This study demonstrates that PGI2 can reverse key platelet functions after their initial activation and identifies a novel mechanism for controlling thrombosis.
High performance micro-flow cytometer based on optical fibres
Authors: Etcheverry S. , Faridi A. , Ramachandraiah H. , Kumar T. , Margulis W. , Laurell F. , Russom A. 
Published: July 2017

AbstractFlow cytometry is currently the gold standard for analysis of cells in the medical laboratory and biomedical research. Fuelled by the need of point-of-care diagnosis, a significant effort has been made to miniaturize and reduce cost of flow cytometers. However, despite recent advances, current microsystems remain less versatile and much slower than their large-scale counterparts. In this work, an all-silica fibre microflow cytometer is presented that measures fluorescence and scattering from particles and cells. It integrates cell transport in circular capillaries and light delivery by optical fibres. Single-stream cell focusing is performed by Elasto-inertial microfluidics to guarantee accurate and sensitive detection. The capability of this technique is extended to high flow rates (up to 800 µl/min), enabling a throughput of 2500 particles/s. The robust, portable and low-cost system described here could be the basis for a point-of-care flow cytometer with a performance comparable to commercial systems.
Population structure of an orchid mycorrhizal fungus with genus-wide specificity
Authors: Ruibal M. P. , Triponez Y. , Smith L. M. , Peakall R. , Linde C. C. 
Published: July 2017

AbstractFundamental life history processes of mycorrhizal fungi with inconspicuous fruiting bodies can be difficult to elucidate. In this study we investigated the species identities and life history of the orchid mycorrhizal Tulasnella fungi, which associate with the south eastern Australia orchid genus Chiloglottis. Tulasnella prima was the primary partner and was found to be associated with all 17 Chiloglottis species across a range of >1000 km, and to occur in the two edaphic conditions investigated (soil and sphagnum hammocks). Another Tulasnella species (T. sphagneti) appears to be restricted to moist conditions of alpine sphagnum hammocks. The population genetic structure of the widespread species T. prima, was investigated at 10 simple sequence repeat (SSR) markers and at four cross-amplified SSR loci for T. sphagneti. For both taxa, no sharing of multilocus genotypes was found between sites, but clones were found within sites. Evidence for inbreeding within T. prima was found at 3 of 5 sites. Significant genetic differentiation was found within and between taxa. Significant local positive spatial genetic autocorrelation was detected among non-clonal isolates at the scale of two metres. Overall, the population genetic patterns indicated that in Tulasnella mating occurs by inbreeding and dispersal is typically restricted to short-distances.
Clinical Significance and Effect of lncRNA HOXA11-AS in NSCLC: A Study Based on Bioinformatics, In Vitro and in Vivo Verification
Authors: Zhang Yu , Chen Wen-jie , Gan Ting-qing , Zhang Xiu-ling , Xie Zu-cheng , Ye Zhi-hua , Deng Yun , Wang Ze-feng , Cai Kai-teng , Li Shi-kang , Luo Dian-zhong , Chen Gang 
Published: July 2017

AbstractHOXA11 antisense RNA (HOXA11-AS) has been shown to be involved in tumorigenesis and development of different cancers. However, the role of HOXA11-AS in non-small cell lung cancer (NSCLC) remains unclear. In this study, we firstly explored and confirmed the expression of HOXA11-AS in NSCLC tissues and cells. Cytometry, CCK-8, cell scratch, migration, Matrigel invasion and flow cytometry assays were performed to determine the biological impact of HOXA11-AS in vitro. Furthermore, a chick embryo chorioallantoic membrane (CAM) model of NSCLC was constructed to explore the effect of HOXA11-AS on tumorigenicity and angiogenesis in vivo. Additionally, bioinformatics analyses were performed to investigate the prospective pathways of HOXA11-AS co-expressed genes. As results, HOXA11-AS was markedly highly expressed in NSCLC tissues and cells. Furthermore, the proliferation, migration, invasion, tumorigenic and angiogenic ability of NSCLC cells were all inhibited and apoptosis was induced after HOXA11-AS knock-down. HOXA11-AS RNAi also led to cell cycle arrest on G0/G1 or G2/M phase. In addition, the non-small cell lung cancer pathway might be involved in regulating the co-expressed genes of HOXA11-AS in NSCLC. These results indicate that HOXA11-AS plays pivotal roles in NSCLC and it can become a novel therapeutic direction for treating NSCLC.
A Drug Carrier for Sustained Zero-Order Release of Peptide Therapeutics
Authors: Zhao Ya-Nan , Xu Xiaoyu , Wen Na , Song Rui , Meng Qingbin , Guan Ying , Cheng Siqi , Cao Danni , Dong Yansheng , Qie Jiankun , Liu Keliang , Zhang Yongjun 
Published: July 2017

AbstractPeptides have great potential as therapeutic agents, however, their clinic applications are severely hampered by their instability and short circulation half-life. Zero-order release carriers could not only extend the circulation lifetime of peptides, but also maintain the plasma drug level constant, and thus maximize their therapeutic efficacy and minimize their toxic effect. Here using PEGylated salmon calcitonin (PEG-sCT)/tannic acid (TA) film as an example, we demonstrated that hydrogen-bonded layer-by-layer films of a PEGylated peptide and a polyphenol could be a platform for zero-order peptide release. The films were fabricated under mild conditions. The second component, TA, is a natural product and presents potential therapeutic activities itself. Unlike common carriers, the new carrier releases the peptide via gradual disintegration of the film because of its dynamic nature. The release of PEG-sCT follows a perfect zero-order kinetics without initial burst release. In addition the release rate could be tuned via external stimuli, such as pH and temperature. When implanted in rats, the films could remain the plasma level of PEG-sCT constant over an extended period. Accordingly, the serum calcium level was reduced and maintained constant over the same period, suggesting an improved therapeutic efficacy of the released drug.