bluuebunny/crossref_metadata_2025 huggingface dataset:
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

In 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

Proton 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

Emergence 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

Muscle 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

Thermal 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

Chinese 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

For 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

Glioma 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

In 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

Humans 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

Prostacyclin (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

Flow 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

Fundamental 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

HOXA11 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

Peptides 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.
Activin signaling is an essential component of the TGF-β induced pro-metastatic phenotype in colorectal cancer
Authors: Staudacher Jonas J. , Bauer Jessica , Jana Arundhati , Tian Jun , Carroll Timothy , Mancinelli Georgina , Özden Özkan , Krett Nancy , Guzman Grace , Kerr David , Grippo Paul , Jung Barbara
Published: July 2017

Advanced colorectal cancer (CRC) remains a critical health care challenge worldwide. Various TGF-β superfamily members are important in colorectal cancer metastasis, but their signaling effects and predictive value have only been assessed in isolation. Here, we examine cross-regulation and combined functions of the two most prominent TGF-β superfamily members activin and TGF-β in advanced colorectal cancer. In two clinical cohorts we observed by immune-based assay that combined serum and tissue activin and TGF-β ligand levels predicts outcome in CRC patients and is superior to single ligand assessment. While TGF-β growth suppression is independent of activin, TGF-β treatment leads to increased activin secretion in colon cancer cells and TGF-β induced cellular migration is dependent on activin, indicating pathway cross-regulation and functional interaction in vitro. mRNA expression of activin and TGF-β pathway members were queried in silico using the TCGA data set. Coordinated ligand and receptor expression is common in solid tumors for activin and TGF-β pathway members. In conclusion, activin and TGF-β are strongly connected signaling pathways that are important in advanced CRC. Assessing activin and TGF-β signaling as a unit yields important insights applicable to future diagnostic and therapeutic interventions.
A comparison of traditional and novel metrics to quantify resistance training
Authors: Marston Kieran J. , Peiffer Jeremiah J. , Newton Michael J. , Scott Brendan R.
Published: July 2017

Common estimates of external training intensity for resistance exercise do not incorporate inter-set recovery duration, and might not reflect the overall demands of training. This study aimed to assess novel metrics of exercise density (ED) during resistance exercise, and how these related to a physiological marker of internal training intensity as well as traditional measures of external training intensity and volume. Thirteen males and seven females performed two bouts of resistance exercise focused on developing strength (5 sets of 5 repetitions with 5-repetition maximum; 180 s recovery) and hypertrophy (3 sets of 10 repetitions with 10-repetition maximum; 60 s recovery). Blood lactate concentration was measured to quantify internal training intensity. Specific metrics of external volume (mechanical work, volume load and total repetitions) and intensity (average weight lifted and ED) were calculated. Despite lower average weights and no difference in mechanical work or volume load, blood lactate was greater following hypertrophy compared with the strength condition. This finding was consistent with higher measures of ED in the hypertrophy compared with the strength condition. Greater ED during hypertrophy resistance exercise, along with the significant association with changes in blood lactate, indicates that ED metrics are reflective of the sessional intensity for resistance exercise.
Individual recognition of opposite sex vocalizations in the zebra finch
Authors: D’Amelio Pietro B. , Klumb Milena , Adreani Mauricio N. , Gahr Manfred L. , ter Maat Andries
Published: July 2017

Individual vocal recognition plays an important role in the social lives of many vocally active species. In group-living songbirds the most common vocalizations during communal interactions are low-intensity, soft, unlearned calls. Being able to tell individuals apart solely from a short call would allow a sender to choose a specific group member to address, resulting in the possibility to form complex communication networks. However, little research has yet been carried out to discover whether soft calls contain individual identity. In this study, males and females of zebra finch pairs were tested with six vocalization types - four different soft calls, the distance call and the male song - to investigate whether they are able to distinguish individuals of the opposite sex. For both sexes, we provide the first evidence of individual vocal recognition for a zebra finch soft unlearned call. Moreover, while controlling for habituation and testing for repeatability of the findings, we quantify the effects of hitherto little studied variables such as partners’ vocal exchange previous to the experiment, spectral content of playback calls and quality of the answers. We suggest that zebra finches can recognize individuals via soft vocalizations, therefore allowing complex directed communication within vocalizing flocks.
The molecular mechanisms of Monascus purpureus M9 responses to blue light based on the transcriptome analysis
Authors: Chen Di , Chen Mianhua , Wu Shufen , Li Zhenjing , Yang Hua , Wang Changlu
Published: July 2017

Light is an important environmental factor that regulates various physiological processes of fungi. To thoroughly study the responses of Monascus to blue light, transcriptome sequencing was performed on mRNAs isolated from samples of Monascus purpureus M9 cultured under three conditions: darkness (D); exposure to blue light for 15 min/d (B15); and exposure to blue light for 60 min/d over 8 days (B60). The number of differentially expressed genes between the three pairs of samples—B15 vs D, B60 vs B15, and B60 vs D—was 1167, 1172, and 220, respectively. KEGG analysis showed the genes involved in primary metabolism including carbon and nitrogen metabolism were downregulated by B15 light treatment, whereas B15 upregulated expression of genes involved with aromatic amino acid metabolism, which associated with development, and branched chain amino acid metabolism, and fatty acid degradation, which can produce the biosynthetic precursors of pigments. When exposed to B60 conditions, genes with roles in carbohydrate metabolism and protein synthesis were upregulated as part of a stress response to blue light. Based on this study, we propose a predicted light-stimulated signal transduction pathway in Monascus. Our work is the first comprehensive investigation concerning the mechanism of Monascus responses to blue light.
Development and Characterization of A Novel Prox1-EGFP Lymphatic and Schlemm’s Canal Reporter Rat
Authors: Jung Eunson , Gardner Daniel , Choi Dongwon , Park Eunkyung , Jin Seong Young , Yang Sara , Castorena-Gonzalez Jorge , Louveau Antoine , Zhou Zhao , Lee Gene K. , Perrault David P. , Lee Sunju , Johnson Maxwell , Daghlian George , Lee Maria , Jin Hong Yeo , Kato Yukinari , Kipnis Jonathan , Davis Michael J. , Wong Alex K. , Hong Young-Kwon
Published: July 2017

The lymphatic system plays a key role in tissue fluid homeostasis, immune cell trafficking, and fat absorption. We previously reported a bacterial artificial chromosome (BAC)-based lymphatic reporter mouse, where EGFP is expressed under the regulation of the Prox1 promoter. This reporter line has been widely used to conveniently visualize lymphatic vessels and other Prox1-expressing tissues such as Schlemm’s canal. However, mice have a number of experimental limitations due to small body size. By comparison, laboratory rats are larger in size and more closely model the metabolic, physiological, and surgical aspects of humans. Here, we report development of a novel lymphatic reporter rat using the mouse Prox1-EGFP BAC. Despite the species mismatch, the mouse Prox1-EGFP BAC enabled a reliable expression of EGFP in Prox1-expressing cells of the transgenic rats and allowed a convenient visualization of all lymphatic vessels, including those in the central nervous system, and Schlemm’s canal. To demonstrate the utility of this new reporter rat, we studied the contractile properties and valvular functions of mesenteric lymphatics, developed a surgical model for vascularized lymph node transplantation, and confirmed Prox1 expression in venous valves. Together, Prox1-EGFP rat model will contribute to the advancement of lymphatic research as a valuable experimental resource.
Neighbor-Neighbor Correlations Explain Measurement Bias in Networks
Authors: Wu Xin-Zeng , Percus Allon G. , Lerman Kristina
Published: July 2017

In numerous physical models on networks, dynamics are based on interactions that exclusively involve properties of a node’s nearest neighbors. However, a node’s local view of its neighbors may systematically bias perceptions of network connectivity or the prevalence of certain traits. We investigate the strong friendship paradox, which occurs when the majority of a node’s neighbors have more neighbors than does the node itself. We develop a model to predict the magnitude of the paradox, showing that it is enhanced by negative correlations between degrees of neighboring nodes. We then show that by including neighbor-neighbor correlations, which are degree correlations one step beyond those of neighboring nodes, we accurately predict the impact of the strong friendship paradox in real-world networks. Understanding how the paradox biases local observations can inform better measurements of network structure and our understanding of collective phenomena.
Effect of LDL cholesterol, statins and presence of mutations on the prevalence of type 2 diabetes in heterozygous familial hypercholesterolemia
Authors: Climent Elisenda , Pérez-Calahorra Sofía , Marco-Benedí Victoria , Plana Nuria , Sánchez Rosa , Ros Emilio , Ascaso Juan F. , Puzo Jose , Almagro Fátima , Lahoz Carlos , Civeira Fernando , Pedro-Botet Juan
Published: July 2017

Patients with heterozygous familial hypercholesterolemia (HeFH) have been reported to be less vulnerable to type 2 diabetes mellitus (T2DM), although the mechanism is unknown. The aims of the present study were to assess the effects of low density lipoprotein (LDL) cholesterol concentration and the presence of FH-causing mutations on T2DM prevalence in HeFH. Data were collected from the Dyslipidemia Registry of the Spanish Arteriosclerosis Society. Inclusion criteria were definite or probable HeFH in patients aged ≥18 years. T2DM prevalence in HeFH patients was compared with data of the general population. 1732 patients were included. The prevalence of T2DM was lower in patients with HeFH compared with the general population (5.94% vs 9.44%; OR: 0.606, 95% CI 0.486–0.755, p < 0.001). Risk factors for developing T2DM were male sex, age, body mass index, hypertension, baseline triglyceride levels and years on statin therapy. The prevalence of T2DM in HeFH patients was 40% lower than that observed in the general population. Gene mutations and LDL cholesterol concentrations were not risk factors associated with the prevalence of T2DM in patients with HeFH. The prevalence of T2DM in patients with HeFH was 40% lower than in the general population matched for age and sex.
How transfer flights shape the structure of the airline network
Authors: Ryczkowski Tomasz , Fronczak Agata , Fronczak Piotr
Published: July 2017

In this paper, we analyse the gravity model in the global passenger air-transport network. We show that in the standard form, the model is inadequate for correctly describing the relationship between passenger flows and typical geo-economic variables that characterize connected countries. We propose a model for transfer flights that allows exploitation of these discrepancies in order to discover hidden subflows in the network. We illustrate its usefulness by retrieving the distance coefficient in the gravity model, which is one of the determinants of the globalization process. Finally, we discuss the correctness of the presented approach by comparing the distance coefficient to several well-known economic events.
Ultra-low threshold polariton lasing at room temperature in a GaN membrane microcavity with a zero-dimensional trap
Authors: Jayaprakash R. , Kalaitzakis F. G. , Christmann G. , Tsagaraki K. , Hocevar M. , Gayral B. , Monroy E. , Pelekanos N. T.
Published: July 2017

Polariton lasers are coherent light sources based on the condensation of exciton-polaritons in semiconductor microcavities, which occurs either in the kinetic or thermodynamic (Bose-Einstein) regime. Besides their fundamental interest, polariton lasers have the potential of extremely low operating thresholds. Here, we demonstrate ultra-low threshold polariton lasing at room temperature, using an all-dielectric, GaN membrane-based microcavity, with a spontaneously-formed zero-dimensional trap. The microcavity is fabricated using an innovative method, which involves photo-electrochemical etching of an InGaN sacrificial layer and allows for the incorporation of optimally-grown GaN active quantum wells inside a cavity with atomically-smooth surfaces. The resulting structure presents near-theoretical Q-factors and pronounced strong-coupling effects, with a record-high Rabi splitting of 64 meV at room-temperature. Polariton lasing is observed at threshold carrier densities 2.5 orders of magnitude lower than the exciton saturation density. Above threshold, angle-resolved emission spectra reveal an ordered pattern in k-space, attributed to polariton condensation at discrete levels of a single confinement site. This confinement mechanism along with the high material and optical quality of the microcavity, accounts for the enhanced performance of our polariton laser, and pave the way for further developments in the area of robust room temperature polaritonic devices.
Rain-induced changes in soil CO2 flux and microbial community composition in a tropical forest of China
Authors: Deng Qi , Hui Dafeng , Chu Guowei , Han Xi , Zhang Quanfa
Published: July 2017

Rain-induced soil CO2 pulse, a rapid excitation in soil CO2 flux after rain, is ubiquitously observed in terrestrial ecosystems, yet the underlying mechanisms in tropical forests are still not clear. We conducted a rain simulation experiment to quantify rain-induced changes in soil CO2 flux and microbial community composition in a tropical forest. Soil CO2 flux rapidly increased by ~83% after rains, accompanied by increases in both bacterial (~51%) and fungal (~58%) Phospholipid Fatty Acids (PLFA) biomass. However, soil CO2 flux and microbial community in the plots without litters showed limited response to rains. Direct releases of CO2 from litter layer only accounted for ~19% increases in soil CO2 flux, suggesting that the leaching of dissolved organic carbon (DOC) from litter layer to the topsoil is the major cause of rain-induced soil CO2 pulse. In addition, rain-induced changes in soil CO2 flux and microbial PLFA biomass decreased with increasing rain sizes, but they were positively correlated with litter-leached DOC concentration rather than total DOC flux. Our findings reveal an important role of litter-leached DOC input in regulating rain-induced soil CO2 pulses and microbial community composition, and may have significant implications for CO2 losses from tropical forest soils under future rainfall changes.
Formation of ionic co-crystals of amphoteric azoles directed by the ionic liquid co-former 1-ethyl-3-methylimidazolium acetate
Authors: Titi Hatem M. , Kelley Steven P. , Easton Max E. , Emerson Stephen D. , Rogers Robin D.
Published: July 2017

Ionic liquid 1-ethyl-3-methylimidazolium acetate as crystallization agent forms ionic co-crystals or new salts with azoles depending on pKa.
Bimolecular-induced hierarchical nanoporous LiTi2(PO4)3/C with superior high-rate and cycling performance
Authors: Sun Wenwei , Liu Jiehua , Liu Xiaoqian , Fan Xiaojing , Zhou Kuan , Wei Xiangfeng
Published: July 2017

Carbon-coated hierarchical LiTi2(PO4)3 was synthesized by a facile bimolecular (glucose and DMEA) assisted hydrothermal reaction and a solid-state reaction, and exhibits excellent high-rate and cycling performance.
Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry
Authors: Morrison Lindsay J. , Chai Wenrui , Rosenberg Jake A. , Henkelman Graeme , Brodbelt Jennifer S
Published: July 2017

Hydrogen-bonding motifs of proteins are deciphered by ultraviolet photodissociation mass spectrometry.
Synthesis and photo-/electro-catalytic properties of a 3D POMOF material based on an interpenetrated copper coordination polymer linked by in situ dual ligands and Dawson-type phosphotungstates
Authors: Fan Ling-yu , Yu Kai , Lv Jing-hua , Zhang He , Su Zhan-hua , Wang Lu , Wang Chun-mei , Zhou Bai-bin
Published: July 2017

A 3D Keggin POMOF based on a unique Cu/pz/pzc MOF was prepared and employed to degradation of typical dyes.
Xanthine oxidase–product complexes probe the importance of substrate/product orientation along the reaction coordinate
Authors: Yang Jing , Dong Chao , Kirk Martin L.
Published: July 2017

Resonance Raman spectroscopy has been used to probe substrate orientation and hydrogen bonding interactions in a xanthine oxidase catalytic intermediate.
3D-printed smartphone-based point of care tool for fluorescence- and magnetophoresis-based cytometry
Authors: Knowlton Stephanie , Joshi Ashwini , Syrrist Philip , Coskun Ahmet F. , Tasoglu Savas
Published: July 2017

We propose a point-of-care-compatible smartphone-based platform for density-based cell sorting via magnetophoresis coupled with fluorescence imaging for versatile medical diagnostics.
Cu(ii)-Mediated keto C(sp3)–H bond α-acyloxylation of N,N-dialkylamides with aromatic carboxylic acids
Authors: Li Wenjing , Yin Changzhen , Yang Xiao , Liu Hailong , Zheng Xueli , Yuan Maolin , Li Ruixiang , Fu Haiyan , Chen Hua
Published: July 2017

The first example of Cu(ii)-mediated oxidative coupling of aromatic carboxylic acids with the C(sp3)–H bond adjacent to the keto group ofN,N-dialkylamides has been developed.
A solution-processed near-infrared polymer: PbS quantum dot photodetectors
Authors: Xu Wenzhan , Peng Hui , Zhu Tao , Yi Chao , Liu Lei , Gong Xiong
Published: July 2017

Operating at room temperature, a solution-processed photodetector with near infrared sensitivity would be a significant advancement towards industrial and scientific applications.
A study of the 160 MeV Ni7+swift heavy ion irradiation effect of defect creation and shifting of the phonon modes on MnxZn1–xO thin films
Authors: Khawal H. A. , Dole B. N.
Published: July 2017

The energy loss to vacancy production shows that the number of vacancies depend on the displacement energy assigned to each target atom element is shown separately.
Cost-effective synthesis of bamboo-structure carbon nanotubes from coal for reversible lithium storage
Authors: Li Jun , Cao Yali , Wang Luxiang , Jia Dianzeng
Published: July 2017

Carbon nanotubes (CNTs) with special structures offers great benefits for energy storage applications.
MOF-derived hierarchical ZnO/ZnFe2O4 hollow cubes for enhanced acetone gas-sensing performance
Authors: Ma Xiang , Zhou Xinyuan , Gong Yan , Han Ning , Liu Haidi , Chen Yunfa
Published: July 2017

A simple and direct pyrolysis of FeIII modified IRMOF-3 is employed to synthesize ZnO/ZnFe2O4 hollow cubes for enhanced acetone gas sensing.
Tuning the fluorescence intensity and stability of porous silicon nanowires via mild thermal oxidation
Authors: Gan Lu , He Haiping , Yu Qianqian , Ye Zhizhen
Published: July 2017

Porous Si nanowires show anomalous luminescence quenching and improved sensing stability upon mild thermal oxidation.
A comparative study of inter- and intramolecular C–H aminations: mechanism and site selectivity
Authors: Wang Juping , Zheng Kangcheng , Lin Binbin , Weng Yuping
Published: July 2017

The similarities and differences of inter- and intramolecular aminations are discussed, with an emphasis on correlation between pathway and site-selectivity.
Niobium-doped titanium dioxide on a functionalized carbon supported palladium catalyst for enhanced ethanol electro-oxidation
Authors: Xu Weichuan , Yan Litao , Wang Huiqiang , Liaw Steven , Luo Hongmei
Published: July 2017

Pd nanoparticles anchored on Nb-doped TiO2 with functionalized carbon support (denoted as Pd/Nb–TiO2–C) is synthesized through a controllable hydrolysis and impregnation method.
Preparation of hollow Nd/TiO2 sub-microspheres with enhanced visible-light photocatalytic activity
Authors: Li Jinlong , Jia Shuaiqiang , Sui Guozhe , Du Lijuan , Li Boxin
Published: July 2017

Hollow Nd/TiO2 sub-microspheres with enhanced visible-light photocatalytic activity are synthesised by employing carbon spheres as the template.
Lignocellulosic fibers: a critical review of the extrusion process for enhancement of the properties of natural fiber composites
Authors: Gallos Antoine , Paës Gabriel , Allais Florent , Beaugrand Johnny
Published: July 2017

This review discusses the extrusion process parameters and their impact on the mechanical properties of composites reinforced with lignocellulosic fibers.
Electric field tunable band-gap crossover in black(blue) phosphorus/g-ZnO van der Waals heterostructures
Authors: Zhang Wei , Zhang Lifa
Published: July 2017

Using hybrid density functional calculations, we studied the electronic and optical properties of graphitic zinc oxide (g-ZnO) and phosphorene van der Waals (vdW) heterostructures.
Algal biomass from the stable growth phase as a potential biosorbent for Pb(ii) removal from water
Authors: Li Yinta , Xia Ling , Huang Rong , Xia Chenggong , Song Shaoxian
Published: July 2017

In this study, the effect of the growth phase on the Pb(ii) removal performance from water usingChlorellasp. QB-102 dry biomass was investigated.
Enhancing the oxygen vacancy formation and migration in bulk chromium(iii) oxide by alkali metal doping: a change from isotropic to anisotropic oxygen diffusion
Authors: Carey John J. , Nolan M.
Published: July 2017

Oxygen vacancy formation and migration are vital properties for reducible oxides such as TiO2, CeO2 and Cr2O3 as the oxygen storage capacity (OSC) of these materials are important for a wide range of applications in photovoltaics, oxidative catalysis and solid oxide fuel cells.
A theoretical study of hybrid lead iodide perovskite homologous semiconductors with 0D, 1D, 2D and 3D structures
Authors: Qian Jingyu , Guo Qing , Liu Leijing , Xu Bin , Tian Wenjing
Published: July 2017

The electrical properties, optical properties and stabilities of hybrid lead iodide perovskite homologous semiconductors with 0D, 1D, 2D and 3D structures have been investigated based on their electronic structures calculated by density functional theory (DFT).
Perspective on carbazole-based organic compounds as emitters and hosts in TADF applications
Authors: Wex Brigitte , Kaafarani Bilal R.
Published: July 2017

Perspective covering carbazole-containing emitters and hosts for third generation TADF (thermally-activated delayed fluorescence) OLED technology along with computational benchmark studies.
CN-Containing donor–acceptor-type small-molecule materials for thermally activated delayed fluorescence OLEDs
Authors: Cao Xudong , Zhang Di , Zhang Shiming , Tao Youtian , Huang Wei
Published: July 2017

Various CN-based TADF materials were demonstrated by changing the donor units, number and relative position of CN-moiety on the π-conjugated bridge.
Protease-activated receptor-2 promotes kidney tubular epithelial inflammation by inhibiting autophagy via the PI3K/Akt/mTOR signalling pathway
Authors: Du Chunyang , Zhang Tao , Xiao Xia , Shi Yonghong , Duan Huijun , Ren Yunzhuo
Published: July 2017

Protease-activated receptor-2 (PAR2), which belongs to a specific class of the G-protein-coupled receptors, is central to several inflammation processes. However, the precise molecular mechanism involved remains undefined. Autophagy has been previously shown to affect inflammation. In the present study, we examine the effect of PAR2 on kidney tubular epithelial autophagy and on autophagy-related inflammation and reveal the underlying mechanism involved. Autophagic activity and levels of autophagic marker LC3 were examined in human kidney tubular epithelial cells with PAR2 knockdown or overexpression. We administered the mammalian target of rapamycin (mTOR) inhibitor (rapamycin) or activator (MHY1485) to investigate the function of the phosphoinositide 3-kinase (PI3K)/Akt/mTOR pathway. We also used transforming growth factor-β1 (TGF-β1)-induced HK-2 cell inflammation models to investigate the role of PAR2-associated autophagy in kidney tubular epithelial inflammation. PAR2 antagonist and rapamycin were administered to mice after unilateral ureteral obstruction to detect the correlations between PAR2, autophagy, and inflammation. Our results show that PAR2 overexpression in HK-2 cells led to a greater reduction in autophagy via the PI3K/Akt/mTOR pathway activation and induces autophagy-related inflammation. Meanwhile, a knockdown of PAR2 via PAR2 RNAi transfection greatly increased autophagy and alleviated autophagy-associated inflammation. In unilateral ureteral obstruction (UUO) kidneys, PAR2 antagonist treatment greatly attenuated renal inflammation and interstitial injury by enhancing autophagy. Moreover, inhibition of mTOR, rapa, markedly increased autophagy and inhibited the UUO-induced inflammation. We conclude that PAR2 induces kidney tubular epithelial inflammation by inhibiting autophagy via the PI3K/Akt/mTOR signalling pathway. Our results are suggestive that PAR2 inhibition may play a role in the treatment of diseases with increased inflammatory responses in renal systems.