bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of an unusual black patina on the Neang Khmau temple (archaeological Khmer area, Cambodia): a multidisciplinary approach
Authors: Casanova Municchia A. , Bartoli F. , Bernardini S. , Caneva G. , Della Ventura G. , Ricci M. A. , Boun Suy T. , Sodo A.
Published: June 2016

In the archaeological Khmer complex (Cambodia), an unusual black patina covering both the exterior and interior walls of the Neang Khmau temple, has been observed during a recent conservative survey. In fact, it is present over all the four facades of the temple, covers a relevant part of the vertical surfaces protected from rainfall and is also homogeneously distributed on the interior of the monument. The upper and the lower areas show, on the contrary, a relevant lichen growth. The temple was built by using laterite bricks, a natural material common in tropical areas as a weathering product of pre‐existing rocks. A preliminary investigation on the patina samples together with ecological considerations excluded a biological origin of the black alteration, thus prompting a more detailed study. In this work, we have investigated the physico‐chemical origin of this unusual patina by identifying its mineralogical and chemical composition. Raman and FTIR spectroscopies, SEM‐EDS, micro‐XRF and XRPD have been applied to characterize the alteration products. Analyses have been performed both on single fragments and on polished cross sections collected from all four temple facades and from one area in the temple interior. Optical observations of the cross sections have evidenced irregularities in the thickness of the patina. Raman and FTIR spectra have revealed that the black layers are mainly composed of manganese minerals (hollandite, romanechite and manganite). This peculiar alteration pattern is interpreted as because of the tropical climatic conditions of Cambodia. Indeed the variation of wet and dry seasons favours the migration of iron and manganese ions and their successive immobilization in regions not directly subject to leaching. Copyright © 2016 John Wiley & Sons, Ltd.
Taste Receptors: Regulators of Sinonasal Innate Immunity
Authors: Carey Ryan M. , Adappa Nithin D. , Palmer James N. , Lee Robert J. , Cohen Noam A.
Published: June 2016

Taste receptors in the oral cavity guide our preferences for foods, preventing toxic ingestions and encouraging proper nutrient consumption. More recently, expression of taste receptors has been demonstrated in other locations throughout the body, including the airway, gastrointestinal tract, pancreas, and brain. The extent and specific roles of extraoral taste receptors are largely unknown, but a growing body of evidence suggests that taste receptors in the airway serve a critical role in sensing bacteria and regulating innate immunity. This review will focus on the function of bitter and sweet taste receptors in the human airway, with particular emphasis on T2R38, a bitter taste receptor found in sinonasal ciliated cells, and the bitter and sweet receptors found on specialized sinonasal solitary chemosensory cells. The importance of these novel taste receptor‐immune circuits in the human airway and their clinical relevance in airway disease will also be reviewed.
Possible association of diazotrophs with marine zooplankton in the Pacific Ocean
Authors: Azimuddin Kazi Md. , Hirai Junya , Suzuki Shotaro , Haider Md. Nurul , Tachibana Aiko , Watanabe Keigo , Kitamura Minoru , Hashihama Fuminori , Takahashi Kazutaka , Hamasaki Koji
Published: June 2016

Dinitrogen fixation, the biological reduction in N2 gas to ammonia contributes to the supply of new nitrogen in the surface ocean. To understand the diversity and abundance of potentially diazotrophic (N2 fixing) microorganisms associated with marine zooplankton, especially copepods, the nifH gene was studied using zooplankton samples collected in the Pacific Ocean. In total, 257 nifH sequences were recovered from 23 nifH‐positive DNA extracts out of 90 copepod samples. The nifH genes derived from cyanobacteria related to Trichodesmium, α‐ and γ‐subdivisions of proteobacteria, and anaerobic euryarchaeota related to Methanosaeta concilii were detected. Our results indicated that Pleuromamma, Pontella, and Euchaeta were the major copepod genera hosting dinitrogen fixers, though we found no species‐specific association between copepods and dinitrogen fixers. Also, the digital PCR provided novel data on the number of copies of the nifH gene in individual copepods, which we report the range from 30 to 1666 copies per copepod. This study is the first systematic study of zooplankton‐associated diazotrophs, covering a large area of the open ocean, which provide a clue to further study of a possible new hotspot of N2 fixation.
Pseudomonas aeruginosa in premise plumbing of large buildings
Authors: Bédard Emilie , Prévost Michèle , Déziel Eric
Published: June 2016

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that is widely occurring in the environment and is recognized for its capacity to form or join biofilms. The present review consolidates current knowledge on P. aeruginosa ecology and its implication in healthcare facilities premise plumbing. The adaptability of P. aeruginosa and its capacity to integrate the biofilm from the faucet and the drain highlight the role premise plumbing devices can play in promoting growth and persistence. A meta‐analysis of P. aeruginosa prevalence in faucets (manual and electronic) and drains reveals the large variation in device positivity reported and suggest the high variability in the sampling approach and context as the main reason for this variation. The effects of the operating conditions that prevail within water distribution systems (disinfection, temperature, and hydraulic regime) on the persistence of P. aeruginosa are summarized. As a result from the review, recommendations for proactive control measures of water contamination by P. aeruginosa are presented. A better understanding of the ecology of P. aeruginosa and key influencing factors in premise plumbing are essential to identify culprit areas and implement effective control measures.
A mixed radiotherapy and chemotherapy model for treatment of cancer with metastasis
Authors: Ghaffari A. , Bahmaie B. , Nazari M.
Published: June 2016

In this paper, a mathematical model of cancer treatment, in the form of a system of ordinary differential equations, by chemotherapy and radiotherapy where there is metastasis from a primary to a secondary site has been proposed and analyzed. The interaction between immune cells and cancer cells has been examined, and the chemotherapy agent has been considered as a predator on both normal and cancer cells. The metastasis may be time delayed. For better investigation of the treatment process and based on physical investigation, the immanent effects of inputs on cancer dynamic have been investigated. It is supposed that the interaction between NK cells and tumor cells changes during the chemotherapy. This novel approach is useful not only to gain a broad understanding of the specific system dynamics but also to guide the development of combination therapies. The analysis is carried out both analytically (where possible) and numerically. By considering such immanent effects, the tumor‐free equilibrium point will be stable at the end of treatment, and the tumor can not recur again, and the patient will totally recover. So, the present analysis suggests that a proper treatment method should change the dynamics of the cancer instead of only reducing the population of cancer cells. Copyright © 2016 John Wiley & Sons, Ltd.
Application of averaging techniques to traffic flow theory
Authors: Sainct Rémi , Louis Xavier , Forestier Alain
Published: June 2016

Real traffic data are very versatile and are hard to explain with the so‐called standard fundamental diagram. A simple microscopic model can show that the heterogeneity of traffic results in a reduced mean flow and that the reduction is proportional to the density variance. Standard averaging techniques allow us to evaluate this reduction without having to describe the complex microscopic interactions.

Using a second equation for the variance results in a two‐dimensional hyperbolic system that can be put in conservative form. The Riemann problem is completely solved in the case of a parabolic fundamental diagram, and the solutions are compared with the famous second‐order Aw–Rascle–Zhang model in a simulation of lane reduction. Adding a diffusion term results in entropy production, and the diffusive model is studied as well. Finally, a numerical scheme is used and converges to the analytical solution. Copyright © 2016 John Wiley & Sons, Ltd.
Transfer of Emulsion Polymerization of Styrene and n‐Butyl Acrylate from Semi‐Batch to a Continuous Tubular Reactor
Authors: Rossow Kristina , Bröge Peter , Lüth Fabian Gabriel , Joy Preet , Mhamdi Adel , Mitsos Alexander , Moritz Hans‐Ulrich , Pauer Werner
Published: June 2016

The transfer of a semi‐batch emulsion copolymerization to a single feed continuous recipe is investigated herein. A single feed continuous tubular reactor is used in the presented study in accordance with the requirement of minimizing the number of dosing streams. The correlation between operating parameters and the product properties are experimentally presented for the semi‐batch as well as for the single feed continuous tubular reactor. It is shown that the transfer from semi‐batch to continuous smart‐scale tubular reactor needs to be direct as opposed to via a batch reactor. The particle sizes and molecular masses obtained in the tubular reactor are similar to those of the semi‐batch process. However, the adjustment of the polymer composition is challenging. Using monomer addition as a means to influence chemical composition is not applicable. Thus, in the tubular reactor the chemical composition of the resulting copolymer depends on the initial monomer composition and reaction temperature. Nevertheless, the mass transfer of the emulsion polymerization damps the copolymer composition distribution (CCD) drift for higher initial monomer contents compared to bulk polymerization. It is shown that transfer of a semi‐batch product to a continuous recipe is possible in early stages of process development.

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Heteroleptic complexes of antifungal drugs with the silver ion
Authors: Giulidori Cecilia , Mosconi Natalia , Toplikar Brenda , Vega Marisa , Williams Patricia , Svetaz Laura , Raimondi Marcela , Rizzotto Marcela
Published: June 2016

In spite of a large number of antibiotics and chemotherapeutics available for medical use, the emergence of old and new antibiotic resistance in the last decades revealed a substantial medical need for new classes of antimicrobial agents. In this paper we report the synthesis, characterization by elemental analysis, Fourier transform infrared and Nuclear magnetic resonance spectroscopies, and antifungal properties of two heteroleptic complexes of albendazole (albz) with Ag(I), using KSCN and o‐phenanthroline (phen) as the second ligand, respectively. Both complexes showed a moderate antifungal activity with all the assayed fungi, mainly Candida albicans and Candida tropicalis, that showed no activity against albendazole. Copyright © 2016 John Wiley & Sons, Ltd.
How do passive infrared triggered camera traps operate and why does it matter? Breaking down common misconceptions
Authors: Welbourne Dustin J. , Claridge Andrew W. , Paull David J. , Lambert Andrew
Published: June 2016

The use of passive infrared (PIR) triggered camera traps has dramatically increased in recent decades. Unfortunately, technical descriptions of how PIR triggered camera traps operate have not been sufficiently clear. Descriptions have often been ambiguous or misleading and in several cases are demonstrably wrong. Such descriptions have led to erroneous interpretations of camera trapping data. This short communication clarifies how PIR sensors operate. We clarify how infrared radiation is emitted and transmitted, and we describe the parts of the PIR sensor and how they detect infrared radiation and, by extension, fauna. Several problematic descriptions of PIR sensors are drawn on to highlight flawed descriptions and demonstrate where erroneous interpretations of camera trapping data occurred. By clarifying the language and the description of PIR triggered camera traps, this paper ensures that wildlife researchers and managers using camera traps will avoid flawed interpretations of their data. Avoiding flawed interpretations of data should reduce wasted effort and resources that would otherwise come about as researchers attempt to test flawed hypotheses. Furthermore, this paper provides a thorough technical reference for camera trapping practitioners, which is not present elsewhere in the wildlife research literature.
Absence of CD66a expression is associated with high microvessel density and high histologic grade in hepatocellular carcinoma
Authors: Wu Chun‐Chieh , Yang Sheau‐Fang , Chen Wan‐Tzu , Tsai Hung‐Pei , Luo Chi‐Wen , Chai Chee‐Yin , Yin Hsin Ling
Published: June 2016

Hepatocellular carcinoma (HCC) is a primary malignancy of the liver. Patients with HCC usually have poor prognosis and high mortality. It has been shown that carcinoembryonic antigen‐related cell adhesion molecule 1 (CD66a) regulates cell signaling, proliferation, and tumor growth. The aim of this study is to analyze the expression and possible role of CD66a in HCC. Immunohistochemical staining of CD66a was performed on 86 HCC cases, and microvessel density was evaluated by CD34 immunostaining. The results were further correlated with clinicopathological parameters. For 47 of 86 HCC cases, the CD66a expression showed diffuse membrane or cytoplasmic staining. The other 39 HCC cases revealed loss of CD66a expression. Loss of CD66a expression was statistically significantly associated with large tumor size (p = 0.016), fatty change (p = 0.039), patients with transcatheter arterial embolization (p = 0.007), and high microvessel density (p = 0.036). CD34 expression had no significant association with tumor size, virus infection, histological grade, and capsular invasion. The diffuse and cytoplasmic expression of CD66a may involve the early stage of the HCC, and the loss of CD66a expression indicates tumor progression.
Reduced-order modelling of the flow around a high-lift configuration with unsteady Coanda blowing
Authors: Semaan Richard , Kumar Pradeep , Burnazzi Marco , Tissot Gilles , Cordier Laurent , Noack Bernd R.
Published: June 2016

We propose a hierarchy of low-dimensional proper orthogonal decomposition (POD) models for the transient and post-transient flow around a high-lift airfoil with unsteady Coanda blowing over the trailing edge. The modal expansion comprises actuation modes as a lifting method for wall actuation following Grahamet al.(Intl J. Numer. Meth. Engng, vol. 44 (7), 1999, pp. 945–972) and Kasnakoğluet al.(Intl J. Control, vol. 81 (9), 2008, pp. 1475–1492). A novel element is separate actuation modes for different frequencies. The structure of the dynamic model rests on a Galerkin projection using the Navier–Stokes equations, simplifying mean-field considerations, and a stochastic term representing the background turbulence. The model parameters are identified with a data assimilation (4D-Var) method. We propose a model hierarchy from a linear oscillator explaining the suppression of vortex shedding by blowing to a fully nonlinear model resolving unactuated and actuated transients with steady and high-frequency modulation of blowing. The models’ accuracy is assessed through the mode amplitudes and an estimator for the lift coefficient. The robustness of the model is physically justified, and then observed for the training and the validation dataset.
THE TOPOLOGICAL PIGEONHOLE PRINCIPLE FOR ORDINALS
Authors: HILTON JACOB
Published: June 2016

Given a cardinal κ and a sequence ${\left( {{\alpha _i}} \right)_{i \in \kappa }}$ of ordinals, we determine the least ordinal β (when one exists) such that the topological partition relation$$\beta \to \left( {top\,{\alpha _i}} \right)_{i \in \kappa }^1$$holds, including an independence result for one class of cases. Here the prefix “top” means that the homogeneous set must be of the correct homeomorphism class rather than the correct order type. The answer is linked to the nontopological pigeonhole principle of Milner and Rado.
WEAK DISTRIBUTIVITY IMPLYING DISTRIBUTIVITY
Authors: HATHAWAY DAN
Published: June 2016

Let $B$ be a complete Boolean algebra. We show that if λ is an infinite cardinal and $B$ is weakly (λω, ω)-distributive, then $B$ is (λ, 2)-distributive. Using a similar argument, we show that if κ is a weakly compact cardinal such that $B$ is weakly (2κ, κ)-distributive and $B$ is (α, 2)-distributive for each α < κ, then $B$ is (κ, 2)-distributive.
SMALL UNIVERSAL FAMILIES OF GRAPHS ON ℵω + 1
Authors: CUMMINGS JAMES , DŽAMONJA MIRNA , MORGAN CHARLES
Published: June 2016

We prove that it is consistent that $\aleph _\omega $ is strong limit, $2^{\aleph _\omega } $ is large and the universality number for graphs on $\aleph _{\omega + 1} $ is small. The proof uses Prikry forcing with interleaved collapsing.
Responses ofPoa annuaand three bentgrass species (Agrostisspp.) to adult and larval feeding of annual bluegrass weevil,Listronotus maculicollis(Coleoptera: Curculionidae)
Authors: Kostromytska O.S. , Koppenhöfer A.M.
Published: June 2016

The annual bluegrass weevil (ABW),Listronotus maculicollisKirby, is an economically important pest of short-cut turfgrass in Eastern North America. Wide spread insecticide resistance warrants the development of alternative management strategies for this pest. ABW damage typically occurs in areas with a high percentage of annual bluegrass,Poa annuaL., the preferred ABW host. Damage to bentgrasses,Agrostisspp., is much rarer and usually less severe. To aid the implementation of host plant resistance as an alternative ABW management strategy we investigated the tolerance of three bentgrass species to ABW feeding. Responses ofP. annua, creeping bentgrass,Agrostis stoloniferaL., colonial bentgrass,Agrostis capillarisL., and velvet bentgrass,Agrostis caninaL., to adult and larval feeding were compared in greenhouse experiments. Grass responses were measured as visual damage, dry weight of the grass stems and leaves, color, density and overall grass quality. To determine possible mechanisms of grass tolerance constitutive fiber and silicon content were also determined. The three bentgrass species tolerated 2–3 times higher numbers of ABW adults and larvae thanP. annuabefore displaying any significant quality decrease. Creeping bentgrass had the lowest damage ratings. ABW infestation caused higher plant yield reduction inP. annua(up to 42%) than in bentgrasses. Observed differences among the grass species in fiber and silicon content in the plant tissue are unlikely to play a role in the resistance of bentgrasses to ABW. Our findings clearly show thatA. stoloniferais the best grass species for the implementation of host plant resistance in ABW management.
The efficacy of eye movement desensitization and reprocessing for post-traumatic stress disorder and depression among Syrian refugees: results of a randomized controlled trial
Authors: Acarturk C. , Konuk E. , Cetinkaya M. , Senay I. , Sijbrandij M. , Gulen B. , Cuijpers P.
Published: June 2016

Background

Previous research indicates a high prevalence of post-traumatic stress disorder (PTSD) and depression among refugees. Eye movement desensitization and reprocessing (EMDR) is an effective treatment for PTSD for victims of natural disasters, car accidents or other traumatic events. The current study examined the effect of EMDR on symptoms of PTSD and depression by comparing the treatment with a wait-list control condition in Syrian refugees.

Method

Adult refugees located in Kilis Refugee Camp at the Turkish–Syrian border with a PTSD diagnosis were randomly allocated to either EMDR (n= 37) or wait-list control (n= 33) conditions. All participants were assessed with the Mini-International Neuropsychiatric Interview Plus at pre-intervention, at 1 week after finishing the intervention and at 5 weeks after finishing the intervention. The main outcome measures were the Harvard Trauma Questionnaire (HTQ) and the Impact of Event Scale-Revised. The Beck Depression Inventory and the Hopkins Symptoms Checklist-25 were included as secondary outcome measures. The Trial Registration no. is NCT01847742.

Results

Mixed-model analyses adjusted for the baseline scores indicated a significant effect of group at post-treatment indicating that the EMDR therapy group showed a significantly larger reduction of PTSD symptoms as assessed with the HTQ. Similar findings were found on the other outcome measures. There was no effect of time or group × time interaction on any measure, showing that the difference between the groups at the post-treatment was maintained to the 5-week follow-up.

Conclusions

EMDR may be effective in reducing PTSD and depression symptoms among Syrian refugees with PTSD located in a refugee camp.
Building Roman Lycia: new inscriptions and monuments from the baths and peristyle buildings Ml 1 and Ml 2 at Oinoanda
Authors: Milner N.P.
Published: June 2016

A new building inscription (no. 1) from Oinoanda, found beside the baths building Ml 1 in 2011, dedicates the building to the Roman emperor Vespasian and his sons Titus and Domitian in AD 73. This article places the new find in the setting of the whole building complex, including the adjacent building Ml 2, which is likely to be a palaistra (wrestling-school), though rebuilt over a century later. The inscription supplies new evidence for the date of the governor of Lycia-Pamphylia, Firmus. It also points to the existence of earlier baths, which is compared to other similar indications from elsewhere in Lycia. A second, but illegible, inscription was recorded in 2012, outside a doorway leading from building Ml 1 into the peristyle building Ml 2 (no. 2). A third inscription on a statue base in building Ml 2 was also recorded (no. 3), along with two other illegible statue-base inscriptions (nos 4 and 5). The article places them in the context of the inscribed monuments found earlier at the building complex (nos 6 and 7), which may have included the small building Ml 3, and discusses them in the light of the broader phenomenon of Julio-Claudian and Flavian baths buildings in the region, and the role of the provincial governors and procurators in overseeing such building projects. This allows us to draw some conclusions about the nature and impact of Roman rule in first-century Lycia, which brought within the reach of many Lycian cities piped water, Italian-style bathing and new, improved facilities for the regionally popular heavy athletic sports of boxing, wrestling and pankration (unarmed combat).
A scoping review of bereavement service outcomes
Authors: Wilson Donna M. , Dhanji Nurin , Playfair Robyn , Nayak Sahana Srinivas , Puplampu Gideon L. , Macleod Rod
Published: June 2016

Objective:

This scoping literature review, through finding and assessing researched bereavement service outcomes, sought to determine the state of bereavement services evaluation, to catalogue service types, and to identify which service or services, if any, demonstrate clear evidence of effectiveness.

Method:

Our methods included: (1) a literature search for published English-language research articles from 2005–2015; (2) critical appraisal of articles to identify findings; (3) compilation of findings; and (4) determination of the relevance of our findings.

Results:

Some 38 papers were found, and all were retained to identify the outcomes researched and research findings. Many different outcomes were studied in the 18 quantitative, 11 qualitative, and 9 mixed-methods investigations undertaken worldwide. Ten studies focused on level of grief, six on stress/distress level, six on grief knowledge, six on level of depression, and five on somatization or physical symptoms. Most commonly, a group of bereavement services was evaluated as a whole, followed by group therapy, individual counseling, written information, and other less common services. No group of services or individual service was determined to yield clear and convincing evidence of effectiveness. Regardless, all but one service were shown to have value—most often related to gaining grief information and/or emotional support. Until high-quality research studies have repeatedly revealed evidence of effectiveness, it is possible that the positive outcomes of bereavement services will be largely based on bereaved people receiving helpful educational information and emotional support from organizations and people prepared to help them.

Significance of results:

This project outlines existing bereavement service types and the state of science in relation to determination of outcomes. It offers suggestions to advance the state of science to validate or refine bereavement services. It brings to light the issue that bereavement service outcomes need to be carefully researched so that evidence can drive service refinement and expansion. It also highlights the importance of effective bereavement services.
Cross-cultural measurement invariance of the Revised Child Anxiety and Depression Scale across 11 world-wide societies
Authors: Stevanovic D. , Bagheri Z. , Atilola O. , Vostanis P. , Stupar D. , Moreira P. , Franic T. , Davidovic N. , Knez R. , Nikšić A. , Dodig-Ćurković K. , Avicenna M. , Multazam Noor I. , Nussbaum L. , Deljkovic A. , Aziz Thabet A. , Petrov P. , Ubalde D. , Monteiro L. A. , Ribas R.
Published: June 2016

Background.

In order to compare estimates by one assessment scale across various cultures/ethnic groups, an important aspect that needs to be demonstrated is that its construct across these groups is invariant when measured using a similar and simultaneous approach (i.e., demonstrated cross-cultural measurement invariance). One of the methods for evaluating measurement invariance is testing for differential item functioning (DIF), which assesses whether different groups respond differently to particular items. The aim of this study was to evaluate the cross-cultural measurement invariance of the Revised Child Anxiety and Depression Scale (RCADS) in societies with different socioeconomic, cultural, and religious backgrounds.

Methods.

The study was organised by the International Child Mental Health Study Group. Self-reported data were collected from adolescents residing in 11 countries: Brazil, Bulgaria, Croatia, Indonesia, Montenegro, Nigeria, Palestinian Territories, the Philippines, Portugal, Romania and Serbia. The multiple-indicators multiple-causes model was used to test the RCADS items for DIF across the countries.

Results.

Ten items exhibited DIF considering all cross-country comparisons. Only one or two items were flagged with DIF in the head-to-head comparisons, while there were three to five items flagged with DIF, when one country was compared with the others. Even with all cross-culturally non-invariant items removed from nine language versions tested, the original factor model representing six anxiety and depressive symptoms subscales was not significantly violated.

Conclusions.

There is clear evidence that relatively small number of the RCADS items is non-invariant, especially when comparing two different cultural/ethnic groups, which indicates on its sound cross-cultural validity and suitability for cross-cultural comparisons in adolescent anxiety and depressive symptoms.
Deep sequencing and in silico analyses identify MYB-regulated gene networks and signaling pathways in pancreatic cancer
Authors: Azim Shafquat , Zubair Haseeb , Srivastava Sanjeev K. , Bhardwaj Arun , Zubair Asif , Ahmad Aamir , Singh Seema , Khushman Moh’d. , Singh Ajay P.
Published: June 2016

We have recently demonstrated that the transcription factor MYB can modulate several cancer-associated phenotypes in pancreatic cancer. In order to understand the molecular basis of these MYB-associated changes, we conducted deep-sequencing of transcriptome of MYB-overexpressing and -silenced pancreatic cancer cells, followed by in silico pathway analysis. We identified significant modulation of 774 genes upon MYB-silencing (p < 0.05) that were assigned to 25 gene networks by in silico analysis. Further analyses placed genes in our RNA sequencing-generated dataset to several canonical signalling pathways, such as cell-cycle control, DNA-damage and -repair responses, p53 and HIF1α. Importantly, we observed downregulation of the pancreatic adenocarcinoma signaling pathway in MYB-silenced pancreatic cancer cells exhibiting suppression of EGFR and NF-κB. Decreased expression of EGFR and RELA was validated by both qPCR and immunoblotting and they were both shown to be under direct transcriptional control of MYB. These observations were further confirmed in a converse approach wherein MYB was overexpressed ectopically in a MYB-null pancreatic cancer cell line. Our findings thus suggest that MYB potentially regulates growth and genomic stability of pancreatic cancer cells via targeting complex gene networks and signaling pathways. Further in-depth functional studies are warranted to fully understand MYB signaling in pancreatic cancer.
Network Modeling Identifies Patient-specific Pathways in Glioblastoma
Authors: Tuncbag Nurcan , Milani Pamela , Pokorny Jenny L. , Johnson Hannah , Sio Terence T. , Dalin Simona , Iyekegbe Dennis O. , White Forest M. , Sarkaria Jann N. , Fraenkel Ernest
Published: June 2016

Glioblastoma is the most aggressive type of malignant human brain tumor. Molecular profiling experiments have revealed that these tumors are extremely heterogeneous. This heterogeneity is one of the principal challenges for developing targeted therapies. We hypothesize that despite the diverse molecular profiles, it might still be possible to identify common signaling changes that could be targeted in some or all tumors. Using a network modeling approach, we reconstruct the altered signaling pathways from tumor-specific phosphoproteomic data and known protein-protein interactions. We then develop a network-based strategy for identifying tumor specific proteins and pathways that were predicted by the models but not directly observed in the experiments. Among these hidden targets, we show that the ERK activator kinase1 (MEK1) displays increased phosphorylation in all tumors. By contrast, protein numb homolog (NUMB) is present only in the subset of the tumors that are the most invasive. Additionally, increased S100A4 is associated with only one of the tumors. Overall, our results demonstrate that despite the heterogeneity of the proteomic data, network models can identify common or tumor specific pathway-level changes. These results represent an important proof of principle that can improve the target selection process for tumor specific treatments.
Transcriptome profiling of the rat retina after optic nerve transection
Authors: Yasuda Masayuki , Tanaka Yuji , Omodaka Kazuko , Nishiguchi Koji M. , Nakamura Orie , Tsuda Satoru , Nakazawa Toru
Published: June 2016

Glaucoma is a group of eye diseases characterized by alterations in the contour of the optic nerve head (ONH), with corresponding visual field defects and progressive loss of retinal ganglion cells (RGCs). This progressive RGC death is considered to originate in axonal injury caused by compression of the axon bundles in the ONH. However, the molecular pathomechanisms of axonal injury-induced RGC death are not yet well understood. Here, we used RNA sequencing (RNA-seq) to examine transcriptome changes in rat retinas 2 days after optic nerve transection (ONT) and then used computational techniques to predict the resulting alterations in the transcriptional regulatory network. RNA-seq revealed 267 differentially expressed genes after ONT, 218 of which were annotated and 49 unannotated. We also identified differentially expressed transcripts, including potentially novel isoforms. Anin silicopathway analysis predicted that CREB1 was the most significant upstream regulator. Thus, this study identified genes and pathways that may be involved in the pathomechanisms of axonal injury. We believe that our data should serve as a valuable resource to understand the molecular processes that define axonal injury-driven RGC death and to discover novel therapeutic targets for glaucoma.
Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium
Authors: Jia Nan , Ding Ming-Zhu , Gao Feng , Yuan Ying-Jin
Published: June 2016

Bacillus thuringiensis and Bacillus endophyticus both act as the companion bacteria, which cooperate with Ketogulonigenium vulgare in vitamin C two-step fermentation. Two Bacillus species have different morphologies, swarming motility and 2-keto-L-gulonic acid productivities when they co-culture with K. vulgare. Here, we report the complete genome sequencing of B. thuringiensis Bc601 and eight plasmids of B. endophyticus Hbe603, and carry out the comparative genomics analysis. Consequently, B. thuringiensis Bc601, with greater ability of response to the external environment, has been found more two-component system, sporulation coat and peptidoglycan biosynthesis related proteins than B. endophyticus Hbe603, and B. endophyticus Hbe603, with greater ability of nutrients biosynthesis, has been found more alpha-galactosidase, propanoate, glutathione and inositol phosphate metabolism, and amino acid degradation related proteins than B. thuringiensis Bc601. Different ability of swarming motility, response to the external environment and nutrients biosynthesis may reflect different companion mechanisms of two Bacillus species. Comparative genomic analysis of B. endophyticus and B. thuringiensis enables us to further understand the cooperative mechanism with K. vulgare, and facilitate the optimization of bacterial consortium.
Mantle Subduction and Uplift of Intracontinental Mountains: A Case Study from the Chinese Tianshan Mountains within Eurasia
Authors: Li Jinyi , Zhang Jin , Zhao Xixi , Jiang Mei , Li Yaping , Zhu Zhixin , Feng Qianwen , Wang Lijia , Sun Guihua , Liu Jianfeng , Yang Tiannan
Published: June 2016

The driving mechanism that is responsible for the uplift of intracontinental mountains has puzzled geologists for decades. This study addresses this issue by using receiver function images across the Chinese Tianshan Mountains and available data from both deep seismic profiles and surface structural deformation. The near-surface structural deformation shows that the Tianshan crust experienced strong shortening during the Cenozoic. The receiver function image across the Tianshan Mountains reveals that the lithosphere of the Junggar Basin to the north became uncoupled along the Moho and the mantle below the Moho subducted southwards beneath the northern part of the Tianshan Mountains, thereby thickening the overlying crust. Similar deep structures, however, are not observed under the Tarim Basin and the adjacent southern Tianshan Mountains. This difference in the deep structures correlates with geomorphological features in the region. Thus, a new model of mantle subduction, herein termed M-type subduction, is proposed for the mountain-building processes in intracontinental compressional settings. The available geomorphological, geological and seismic data in the literatures show that this model is probably suitable for other high, linear mountains within the continent.
Informational laws of genome structures
Authors: Bonnici Vincenzo , Manca Vincenzo
Published: June 2016

In recent years, the analysis of genomes by means of strings of lengthkoccurring in the genomes, calledk-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value ofkfor applying information theoretic concepts that express intrinsic aspects of genomes. The valuek = lg2(n), wherenis the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balancesentropicandanti-entropiccomponents of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.
Steady State Ocean Response to Wind Forcing in Extratropical Frontal Regions
Authors: Cronin Meghan F. , Tozuka Tomoki
Published: June 2016

In regions of strong sea surface temperature (SST) gradients, the surface “geostrophic” currents have a vertical shear aligned with the surface density front defined by the temperature. This surface geostrophic (“thermal wind”) shear can balance a portion of the surface wind stress, altering the classic Ekman response to wind forcing. Here we show that these frontal effects cannot be ignored in the Tropics or in strong frontal regions in the extratropics, such as found in coastal regions and in western boundary currents of all basins. Frontal effects also dominate the classic Ekman response in the regions of both hemispheres where Trade winds change to westerlies. Implications for vertical motion and global heat transport are discussed.
Modelling how incorporation of divalent cations affects calcite wettability–implications for biomineralisation and oil recovery
Authors: Andersson M. P. , Dideriksen K. , Sakuma H. , Stipp S. L. S.
Published: June 2016

Using density functional theory and geochemical speciation modelling, we predicted how solid-fluid interfacial energy is changed, when divalent cations substitute into a calcite surface. The effect on wettability can be dramatic. Trace metal uptake can impact organic compound adsorption, with effects for example, on the ability of organisms to control crystal growth and our ability to predict the wettability of pore surfaces. Wettability influences how easily an organic phase can be removed from a surface, either organic compounds from contaminated soil or crude oil from a reservoir. In our simulations, transition metals substituted exothermically into calcite and more favourably into sites at the surface than in the bulk, meaning that surface properties are more strongly affected than results from bulk experiments imply. As a result of divalent cation substitution, calcite-fluid interfacial energy is significantly altered, enough to change macroscopic contact angle by tens of degrees. Substitution of Sr, Ba and Pb makes surfaces more hydrophobic. With substitution of Mg and the transition metals, calcite becomes more hydrophilic, weakening organic compound adsorption. For biomineralisation, this provides a switch for turning on and off the activity of organic crystal growth inhibitors, thereby controlling the shape of the associated mineral phase.
Non-canonical NFκB activation promotes chemokine expression in podocytes
Authors: Valiño-Rivas Lara , Gonzalez-Lafuente Laura , Sanz Ana B. , Ruiz-Ortega Marta , Ortiz Alberto , Sanchez-Niño Maria D.
Published: June 2016

TNF-like weak inducer of apoptosis (TWEAK) receptor Fn14 is expressed by podocytes and Fn14 deficiency protects from experimental proteinuric kidney disease. However, the downstream effectors of TWEAK/Fn14 in podocytes are poorly characterized. We have explored TWEAK activation of non-canonical NFκB signaling in cultured podocytes. In cultured podocytes, TWEAK increased the expression of the chemokines CCL21, CCL19 and RANTES in a time-dependent manner. The inhibitor of canonical NFκB activation parthenolide inhibited the CCL19 and the early RANTES responses, but not the CCL21 or late RANTES responses. In this regard, TWEAK induced non-canonical NFκB activation in podocytes, characterized by NFκB2/p100 processing to NFκB2/p52 and nuclear migration of RelB/p52. Silencing by a specific siRNA of NIK, the upstream kinase of the non-canonical NFκB pathway, prevented CCL21 upregulation but did not modulate CCL19 or RANTES expression in response to TWEAK, thus establishing CCL21 as a non-canonical NFκB target in podocytes. Increased kidney Fn14 and CCL21 expression was also observed in rat proteinuric kidney disease induced by puromycin and was localized to podocytes. In conclusion, TWEAK activates the non-canonical NFκB pathway in podocytes, leading to upregulation of CCL21 expression. The non-canonical NFκB pathway should be explored as a potential therapeutic target in proteinuric kidney disease.
Membrane protein assembly: two cytoplasmic phosphorylated serine sites of Vpu from HIV-1 affect oligomerization
Authors: Chen Chin-Pei , Lin Meng-Han , Chan Ya-Ting , Chen Li-Chyong , Ma Che , Fischer Wolfgang B.
Published: June 2016

Viral protein U (Vpu) encoded by human immunodeficiency virus type 1 (HIV-1) is a short integral membrane protein which is known to self-assemble within the lipid membrane and associate with host factors during the HIV-1 infectivity cycle. In this study, full-length Vpu (M group) from clone NL4-3 was over-expressed in human cells and purified in an oligomeric state. Various single and double mutations were constructed on its phosphorylation sites to mimic different degrees of phosphorylation. Size exclusion chromatography of wild-type Vpu and mutants indicated that the smallest assembly unit of Vpu was a dimer and over time Vpu formed higher oligomers. The rate of oligomerization increased when (i) the degree of phosphorylation at serines 52 and 56 was decreased and (ii) when the ionic strength was increased indicating that the cytoplasmic domain of Vpu affects oligomerization. Coarse-grained molecular dynamic simulations with models of wild-type and mutant Vpu in a hydrated lipid bilayer supported the experimental data in demonstrating that, in addition to a previously known role in downregulation of host factors, the phosphorylation sites of Vpu also modulate oligomerization.
Optofluidic UV-Vis spectrophotometer for online monitoring of photocatalytic reactions
Authors: Wang Ning , Tan Furui , Zhao Yu , Tsoi Chi Chung , Fan Xudong , Yu Weixing , Zhang Xuming
Published: June 2016

On-chip integration of optical detection units into the microfluidic systems for online monitoring is highly desirable for many applications and is also well in line with the spirit of optofluidics technology–fusion of optics and microfluidics for advanced functionalities. This paper reports the construction of a UV-Vis spectrophotometer on a microreactor, and demonstrates the online monitoring of the photocatalytic degradations of methylene blue and methyl orange under different flow rates and different pH values by detecting the intensity change and/or the peak shift. The integrated device consists of a TiO2-coated glass substrate, a PDMS micro-sized reaction chamber and two flow cells. By comparing with the results of commercial equipment, we have found that the measuring range and the sensitivity are acceptable, especially when the transmittance is in the range of 0.01–0.9. This integrated optofluidic device can significantly cut down the test time and the sample volume, and would provide a versatile platform for real-time characterization of photochemical performance. Moreover, its online monitoring capability may enable to access the usually hidden information in biochemical reactions like intermediate products, time-dependent processes and reaction kinetics.
Genome-wide characterization of the β-1,3-glucanase gene family in Gossypium by comparative analysis
Authors: Xu Xiaoyang , Feng Yue , Fang Shuai , Xu Jun , Wang Xinyu , Guo Wangzhen
Published: June 2016

The β-1,3-glucanase gene family is involved in a wide range of plant developmental processes as well as pathogen defense mechanisms. Comprehensive analyses of β-1,3-glucanase genes (GLUs) have not been reported in cotton. Here, we identified 67, 68, 130 and 158 GLUs in four sequenced cotton species, G. raimondii (D5), G. arboreum (A2), G. hirsutum acc. TM-1 (AD1) and G. barbadense acc. 3–79 (AD2), respectively. Cotton GLUs can be classified into the eight subfamilies (A–H) and their protein domain architecture and intron/exon structure are relatively conserved within each subfamily. Sixty-seven GLUs in G. raimondii were anchored onto 13 chromosomes, with 27 genes involved in segmental duplications and 13 in tandem duplications. Expression patterns showed highly developmental and spatial regulation of GLUs in TM-1. In particular, the expression of individual member of GLUs in subfamily E was limited to roots, leaves, floral organs or fibers. Members of subfamily E also showed more protein evolution and subgenome expression bias compared with members of other subfamilies. We clarified that GLU42 and GLU43 in subfamily E were preferentially expressed in root and leaf tissues and significantly upregulated after Verticillium dahliae inoculation. Silencing of GLU42 and GLU43 significantly increased the susceptibility of cotton to V. dahliae.
Long-term non-invasive interrogation of human dorsal root ganglion neuronal cultures on an integrated microfluidic multielectrode array platform
Authors: Enright H. A. , Felix S. H. , Fischer N. O. , Mukerjee E. V. , Soscia D. , Mcnerney M. , Kulp K. , Zhang J. , Page G. , Miller P. , Ghetti A. , Wheeler E. K. , Pannu S.
Published: June 2016

Electrophysiology measurements from human primary neurons after repeated chemical exposures are enabled with an integrated microfluidic and microelectrode array device.
Anion recognition by oligo-(thio)urea-based receptors
Authors: Jia Chuandong , Zuo Wei , Zhang Dan , Yang Xiao-Juan , Wu Biao
Published: June 2016

Recent progress in the construction of metal-coordination-assisted and covalently connected oligourea receptors and their anion coordination chemistry is presented.
Highly solvatochromic and tunable fluorophores based on a 4,5-quinolimide scaffold: novel CDK5 probes
Authors: González-Vera Juan A. , Fueyo-González Francisco , Alkorta Ibon , Peyressatre Marion , Morris May C. , Herranz Rosario
Published: June 2016

Novel 4,5-quinolimide-based solvatochromic fluorophores conjugated to a CDK5 derived peptide demonstrated sensitivity for monitoring CDK5/p25 interaction in living cells.
Relationships between the solution and solid-state properties of solution-cast low-k silica thin films
Authors: Chiang Chao-Ching , Su Chien-You , Yang An-Chih , Wang Ting-Yu , Lee Wen-Ya , Hua Chi-Chung , Kang Dun-Yen
Published: June 2016

This paper reports on the fabrication of low-k (amorphous) silica thin films cast from solutions without and with two different types of surfactants (TWEEN® 80 and Triton™ X-100) to elucidate the relationships between the structural/morphological features of the casting solutions and the physical properties of the resulting thin films.
Inorganic materials acting as heterogeneous photocatalysts and catalysts in the same reactions
Authors: Palmisano L. , García-López E. I. , Marcì G.
Published: June 2016

General considerations on the differences and similarities between heterogeneous photocatalysis and thermal catalysis are presented.
An acid-cleavable phthalocyanine tetramer as an activatable photosensitiser for photodynamic therapy
Authors: Chow Sun Y. S. , Lo Pui-Chi , Ng Dennis K. P.
Published: June 2016

A novel self-quenched phthalocyanine tetramer has been prepared which can be activated in acidic environments, resulting in enhanced fluorescence emission and singlet oxygen production.
Delivery of minimally dispersed liquid interfaces for sequential surface chemistry
Authors: Ostromohov N. , Bercovici M. , Kaigala G. V.
Published: June 2016

Rapid liquid switching on a microfluidic probe enables localized multi-step surface reactions.
Iridium(iii)-catalyzed regioselective direct arylation of sp2 C–H bonds with diaryliodonium salts
Authors: Gao Pan , Liu Li , Shi Zhuangzhi , Yuan Yu
Published: June 2016

A regioselective direct arylation of arenes and olefins at the ortho position is reported.
Catalytic asymmetric direct-type 1,4-addition reactions of simple esters
Authors: Sato Io , Suzuki Hirotsugu , Yamashita Yasuhiro , Kobayashi Shū
Published: June 2016

Catalytic asymmetric 1,4-addition reactions of simple esters have been developed. The desired reactions proceeded smoothly with high enantioselectivities.