bluuebunny/crossref_metadata_2025 huggingface dataset:
Linking the distribution of microbial deposits from the Great Salt Lake
(Utah, USA) to tectonic and climatic processes
Authors: Bouton Anthony , Vennin Emmanuelle , Boulle Julien , Pace Aurélie , Bourillot Raphaël , Thomazo Christophe , Brayard Arnaud , Désaubliaux Guy , Goslar Tomasz , Yokoyama Yusuke , Dupraz Christophe , Visscher Pieter T.
Published: October 2016

Abstract. The Great Salt Lake is a modern hypersaline lake, in which an extended modern and ancient microbial sedimentary system has developed. Detailed mapping based on aerial images and field observations can be used to identify non-random distribution patterns of microbial deposits, such as paleoshorelines associated with extensive polygons or fault-parallel alignments. Although it has been inferred that climatic changes controlling the lake level fluctuations explain the distribution of paleoshorelines and polygons, straight microbial deposit alignments may underline a normal fault system parallel to the Wasatch Front. This study is based on observations over a decimetre to kilometre spatial range, resulting in an integrated conceptual model for the controls on the distribution of the microbial deposits. The morphology, size and distribution of these deposits result mainly from environmental changes (i.e. seasonal to long-term water level fluctuations, particular geomorphological heritage, fault-induced processes, groundwater seepage) and have the potential to bring further insights into the reconstruction of paleoenvironments and paleoclimatic changes through time. New radiocarbon ages obtained on each microbial macrofabric described in this study improve the chronological framework and question the lake level variations that are commonly assumed.
Water availability limits tree productivity, carbon stocks, and carbon
residence time in mature forests across the western United States
Authors: Berner Logan T. , Law Beverly E. , Hudiburg Tara W.
Published: October 2016

Abstract. Much of the western US is projected to become warmer and drier over the coming century, underscoring the need to understand how climate influences terrestrial ecosystems in this region. We quantified the response of tree net primary productivity (NPP), live biomass (BIO), and mean carbon residence time (CRT = BIO/NPP) to spatial variation in climatic water availability in the western US. We used forest inventory measurements from 1,953 mature stands (≥ 100 years) in Washington, Oregon, and California (WAORCA) along with satellite and climate data sets covering the western US. We summarized forest structure and function in both domains along a 400 cm yr−1 hydrologic gradient, quantified with a climate moisture index based on the difference between precipitation and reference evapotranspiration summed from October-September (i.e., water-year) and then averaged annually from 1985–2014 (CMIwy). Median NPP, BIO, and CRT computed at 10 cm yr−1 intervals along the CMIwy gradient increased monotonically with increasing CMIwy across both WAORCA (rs = 0.93–0.96, p
TOWARDS AUTOMATIC SEMANTIC LABELLING OF 3D CITY MODELS
Authors: Rook M. , Biljecki F. , Diakité A. A.
Published: October 2016

Abstract. The lack of semantic information in many 3D city models is a considerable limiting factor in their use, as a lot of applications rely on semantics. Such information is not always available, since it is not collected at all times, it might be lost due to data transformation, or its lack may be caused by non-interoperability in data integration from other sources. This research is a first step in creating an automatic workflow that semantically labels plain 3D city model represented by a soup of polygons, with semantic and thematic information, as defined in the CityGML standard. The first step involves the reconstruction of the topology, which is used in a region growing algorithm that clusters upward facing adjacent triangles. Heuristic rules, embedded in a decision tree, are used to compute a likeliness score for these regions that either represent the ground (terrain) or a RoofSurface. Regions with a high likeliness score, to one of the two classes, are used to create a decision space, which is used in a support vector machine (SVM). Next, topological relations are utilised to select seeds that function as a start in a region growing algorithm, to create regions of triangles of other semantic classes. The topological relationships of the regions are used in the aggregation of the thematic building features. Finally, the level of detail is detected to generate the correct output in CityGML. The results show an accuracy between 85 % and 99 % in the automatic semantic labelling on four different test datasets. The paper is concluded by indicating problems and difficulties implying the next steps in the research.
LADM AND INDOORGML FOR SUPPORT OF INDOOR SPACE IDENTIFICATION
Authors: Zlatanova S. , Van Oosterom P. J. M. , Lee J. , Li K.-J. , Lemmen C. H. J.
Published: October 2016

Abstract. Guidance and security in large public buildings such as airports, museums and shopping malls requires much more information that traditional 2D methods offer. Therefore 3D semantically-reach models have been actively investigated with the aim to gather knowledge about availability and accessibility of spaces. Spaces can be unavailable to specific users because of plenty of reasons: the 3D geometry of spaces (too low, too narrow), the properties of the objects to be guided to a specific part of the building (walking, driving, flying), the status of the indoor environment (e.g. crowded, limited light, under reconstruction), property regulations (private areas), security considerations and so on. However, such information is not explicitly avaible in the existing 3D semantically-reach models. IFC and CityGML are restricted to architectural building components and provide little to no means to describe such properties. IndoorGML has been designed to establish a generic approach for space identification allowing a space subdivision and automatic creation of a network for route computation. But currently it also represents only spaces as they are defined by the architectural layout of the building. The Land Administration Domain Model is currently the only available model to specify spaces on the basis of ownership and rights for use. In this paper we compare the principles of IndoorGML and LADM, investigate the approaches to define spaces and suggest options to the linking of the two types of spaces. We argue that LADM space subdivision on basis of properties and rights of use can be used to define to semantically and geometrically available and accessible spaces and therefore can enrich the IndoorGML concept.
3D PROCEDURAL RECONSTRUCTION OF URBAN LANDSCAPES FOR THE
PURPOSES OF A WEB-BASED HISTORICAL ATLAS
Authors: Cajthaml J. , Tobiáš P.
Published: October 2016

Abstract. The ”Czech Historical Atlas” project is a part of the NAKI II programme of the Czech Ministry of Culture and aims to create the following two main outputs: a printed atlas of the Czech history in the 20th century and an electronic map portal on the Czech history. This paper is focused on the latter mentioned output and specifically on the design of 3D scenes which should supplement the 2D map content. Currently existing literature is briefly reviewed and the procedural modelling is found to be suitable for the needs of urban landscape reconstruction. Furthermore, available data sources in the Czech republic are discussed and important aspects of modelling are presented.
3D DOCUMENTATION AND BIM MODELING OF CULTURAL HERITAGE
STRUCTURES USING UAVS: THE CASE OF THE FOINIKARIA CHURCH
Authors: Themistocleous K. , Agapiou A. , Hadjimitsis D.
Published: October 2016

Abstract. The documentation of architectural cultural heritage sites has traditionally been expensive and labor-intensive. New innovative technologies, such as Unmanned Aerial Vehicles (UAVs), provide an affordable, reliable and straightforward method of capturing cultural heritage sites, thereby providing a more efficient and sustainable approach to documentation of cultural heritage structures. In this study, hundreds of images of the Panagia Chryseleousa church in Foinikaria, Cyprus were taken using a UAV with an attached high resolution camera. The images were processed to generate an accurate digital 3D model by using Structure in Motion techniques. Building Information Model (BIM) was then used to generate drawings of the church. The methodology described in the paper provides an accurate, simple and cost-effective method of documenting cultural heritage sites and generating digital 3D models using novel techniques and innovative methods.
Brief Communication: Capturing scales of spatial heterogeneity of Antarctic sea ice algae communities
Authors: Forrest Alexander L. , Lund-Hansen Lars C. , Sorrell Brian K. , Bowden-Floyd Isak , Lucieer Vanessa , Cossu Remo , Hawes Ian
Published: October 2016

Abstract. Identifying spatial heterogeneity of sea ice algae communities is critical to predicting ecosystem response under future climate scenarios. Using an autonomous robotic sampling platform beneath sea ice in McMurdo Sound, Antarctica, we measured irradiance in spectral bands expected to describe the spatial heterogeneity. Derived estimates of ice algae biomass identified patchiness at length scales varying from 50–70 m under first-year sea ice. These results demonstrate that a step-change in how these communities can be assessed and monitored. The developed methodologies could be subsequently refined to further categorize different ice algae communities and their associated productivity in both Arctic and Antarctic waters.
Optimizing Multi-Item EOQ when the Constraint of Annual Number of Orders is Active
Authors: Ghafour Karzan Mahdi , Rashid Rezan Hama
Published: October 2016

The responsibility in inventory models decides of how much or how many of inventory items to order. An economic order quantity (EOQ) differs from a model to another according to the assumptions and the variables. This paper has developed the EOQ in two deterministic inventory model (Purchases with shortage and production with shortage) of multi-item when the objective function is subjected to annual number of orders. The constraints are assumed to be active if the left hand side does not satisfy the right hand side condition. Thus, Lagrange method is used to find the new multi-item EOQ in each two models with the constraint to achieve the new formula of EOQ. Finally, a numerical example is provided to justify the proposed model.
In-plane switching mode-based liquid-crystal hybrid Si wired Mach–Zehnder optical switch
Authors: Atsumi Yuki , Miyazaki Tetsuo , Takei Ryohei , Okano Makoto , Miura Noboru , Mori Masahiko , Sakakibara Youichi
Published: October 2016

A Mach–Zehnder optical switch based on a Si wire waveguide embedded in a liquid crystal overcladding is developed. Switching operation at a wavelength of 1550 nm with a voltage-length product of 1.86 V·mm is obtained for a device with a 300-µm-long loop-back phase shifter. The switching speed is qualitatively evaluated under various alignment film conditions, and switch-off and switch-on times of 7.9 and 8.4 ms, respectively, are achieved when the alignment layer is appropriately positioned relative to the waveguides.
Identification and temporal expression of putative circadian clock transcripts in the amphipod crustaceanTalitrus saltator
Authors: O’Grady Joseph F. , Hoelters Laura S. , Swain Martin T. , Wilcockson David C.
Published: October 2016

Background

Talitrus saltatoris an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean.T. saltatorexhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species.

Methods

We harvested brain tissue from animals expressing robust circadian activity rhythms and used homology cloning and Illumina RNAseq approaches to sequence and identify the core circadian clock and clock-related genes in these samples. We assessed the temporal expression of these genes in time-course samples from rhythmic animals using RNAseq.

Results

We identified a comprehensive suite of circadian clock gene homologues inT. saltatorincluding the ‘core’ clock genesperiod(Talper),cryptochrome 2(Talcry2),timeless(Taltim),clock(Talclk), andbmal1(Talbmal1). In addition we describe the sequence and putative structures of 23 clock-associated genes including two unusual, extended isoforms of pigment dispersing hormone (Talpdh). We examined time-course RNAseq expression data, derived from tissues harvested from behaviourally rhythmic animals, to reveal rhythmic expression of these genes with approximately circadian period inTalperandTalbmal1. Of the clock-related genes,casein kinase IIβ(TalckIIβ),ebony(Talebony),jetlag(Taljetlag),pigment dispensing hormone(Talpdh),protein phosphatase 1(Talpp1),shaggy(Talshaggy),sirt1(Talsirt1), sirt7 (Talsirt7) and supernumerary limbs (Talslimb) show temporal changes in expression.

Discussion

We report the sequences of principle genes that comprise the circadian clock ofT. saltatorand highlight the conserved structural and functional domains of their deduced cognate proteins. Our sequencing data contribute to the growing inventory of described comparative clocks. Expression profiling of the identified clock genes illuminates tantalising targets for experimental manipulation to elucidate the molecular and cellular control of clock-driven phenotypes in this crustacean.
Harnessing the Lewis Acidity of HFIP through its Cooperation with a Calcium(II) Salt: Application to the Aza‐Piancatelli Reaction
Authors: Lebœuf David , Marin Lucile , Michelet Bastien , Perez‐Luna Alejandro , Guillot Régis , Schulz Emmanuelle , Gandon Vincent
Published: October 2016

A method to extend the scope of the aza‐Piancatelli reaction between 2‐furylcarbinols and anilines is depicted. We found that 1,1,1,3,3,3‐hexafluoro‐2‐propanol (HFIP) is the solvent of choice for this transformation, as it outcompetes the usual solvents in terms of rate and yield. Side reactions and other issues raised by the title reaction are prevented, thereby providing an avenue to complex molecules that were previously inaccessible. Lewis acidity studies and computations were carried out to unveil the role of HFIP. Based on these results, we propose that HFIP is, in fact, acting as a Lewis acid and that its acidity can be enhanced when combined with a calcium(II) salt.
Chiral N,N′‐Dioxide‐Organocatalyzed Regio‐, Diastereo‐ and Enantioselective Michael Addition–Alkylation Reaction
Authors: Feng Juhua , Yuan Xiao , Luo Weiwei , Lin Lili , Liu Xiaohua , Feng Xiaoming
Published: October 2016

A highly regio‐, diastereo‐ and enantioselective Michael addition–alkylation reaction between α‐substituted cyano ketones and (Z)‐bromonitrostyrenes has been realized by using a chiral N,N′‐dioxide as organocatalyst. A variety of substrates performed well in this reaction, and the corresponding multifunctionalized chiral 2,3‐dihydrofurans were obtained in up to 95 % yield with 95:5 dr and 93 % ee.
Poly(N‐isopropylacrylamide‐co‐N‐isopropylmethacrylamide) Thermo‐Responsive Microgels as Self‐Regulated Drug Delivery System
Authors: Fundueanu Gheorghe , Constantin Marieta , Bucatariu Sanda , Ascenzi Paolo
Published: October 2016

Poly(N‐isopropylacrylamide‐co‐N‐isopropylmethacrylamide) (poly(NIPAAm‐co‐NIPMAAm)) is synthesized as an attractive thermo‐responsive copolymer by an original procedure. Due to the similar structure of the two co‐monomers, the poly(NIPAAm‐co‐NIPMAAm) copolymer displays a very sharp phase transition, under physiological conditions (phosphate buffer solution at pH = 7.4). The copolymer, showing the 51/49 co‐monomer NIPAAm/NIPMAAm molar ratio, displays a lower critical solution temperature (LCST) close to that of the human body temperature (36.8 °C). The poly(NIPAAm‐co‐NIPMAAm) microgels obtained at the 51:49 co‐monomer ratio displays a volume phase transition temperature (VPTT) slightly smaller than LCST. The deswelling rate of the microgels is very high (k = 0.019 s−1), the shrinkage occurring almost instantaneously, whereas the swelling rate is slightly lower (k = 0.0077 s−1). The microgels are loaded with the model drug dexamethasone and the drug release is investigated at different temperatures, below and above the VPTT. Under thermal cycling operation between 32 and 38 °C, the pulsatile release of dexamethasone is observed.

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Consideration Set Overvaluation: When Impossibly Favorable Ratings of a Set of Brands Are Observed
Authors: Kardes Frank R. , Sanbonmatsu David M. , Cronley Maria L. , Houghton David C.
Published: October 2016

Consumers often focus on the characteristics of one brand and consider insufficiently the characteristics of other brands. Singular evaluation processes often result in judgments of a focal brand that are more extreme than warranted. This research investigates the extent to which this extremity effect generalizes to a consideration set consisting of multiple brands. Three experiments show that a set of favorably regarded brands is perceived as more favorable than would be possible if the salience manipulation had no effect. In Experiment 1, participants overestimated the likelihood that the best brand in the market was included in the presented set. In Experiment 2, the average rank assigned to the brands in the presented set was inflated. Extreme judgments were observed regardless of whether the focal set of brands was offered by a specialty store with a high‐quality reputation or by a general merchandise store with a low‐quality reputation. In Experiment 3, extreme intentions to buy now from the focal store were reduced when a comparative (vs. singular) judgment task was performed, but only when the need for cognitive closure was low as opposed to high. The results suggest that singular evaluation processes lead to consideration set overvaluation regardless of which particular favorably regarded brands happen to be included in the set.
Development and testing of subsonic tandem deceleration system
Authors: Samani M. , Mahyari M. Faraji
Published: October 2016

For many years, deceleration systems developed in an evolutionary fashion. This evolution needed flight test and experimental data. Concurrently, payload became much more expensive and needed to be safer. Today, there are a variety of methods employed to recover airborne bodies such as bio-capsules, reentry satellites, carrier missiles' boosters, reentry satellites, etc. Most of these methods make use of a parachute landing system in which recovery occurs in multiple phases. This paper studies the final phase of the subsonic recovery scenario for which a multi-phase deceleration system has been designed. To observe and evaluate system performance, a test projectile is designed that accelerates the payload to a certain velocity in order to test the recovery system. Finally, theoretical and test results are compared to indicate the appropriate design and reliable deceleration velocity in a space payload recovery.
Peacekeeping, Compliance with International Norms, and Transactional Sex in Monrovia, Liberia
Authors: Beber Bernd , Gilligan Michael J. , Guardado Jenny , Karim Sabrina
Published: October 2016

United Nations policy forbids its peacekeepers and other personnel from engaging in transactional sex (the exchange of money, favors, or gifts for sex), but we find the behavior to be very common in our survey of Liberian women. Using satellite imagery and GPS locators, we randomly selected 1,381 households and randomly sampled 475 women between the ages of eighteen and thirty. Using an iPod in private to preserve the anonymity of their responses, these women answered sensitive questions about their sexual histories. More than half of them had engaged in transactional sex, a large majority of them (more than 75 percent) with UN personnel. We estimate that each additional battalion of UN peacekeepers caused a significant increase in a woman's probability of engaging in her first transactional sex. Our findings raise the concern that the private actions of UN personnel in the field may set back the UN's broader gender-equality and economic development goals, and raise broader questions about compliance with international norms.
Occurrence and habitat use of Bryde's whales (Balaenoptera edeni) in the Cabo Frio region, South-eastern Brazil
Authors: Maciel Israel S. , Tardin Rodrigo H. , Simão Sheila M.
Published: October 2016

Ninety-six field trips were conducted between summer 2010 and 2012 in order to understand the occurrence and habitat use of Bryde's whale (Balaenoptera edeni) in the Cabo Frio region, South-eastern Brazil. Bryde's whales were present in the study area between November and July, being observed during all seasons, but occur more frequently during the autumn (Nindividuals= 16) and spring (Nindividuals= 13), followed by summer (Nindividuals= 5) and winter (Nindividuals= 2), respectively. Bryde's whales were observed in water depths ranging from 20.1–100 m. Furthermore, during 2240 min of video recordings, the most frequent behaviour observed was foraging (40.2%; 900 min). Travelling comprised 28.1% (630 min) of observations, while in 33.1% (710 min) behaviour could not be determined. Taking into account the pattern of occurrence, the use of deeper bathymetric bins and the frequency observed, the foraging behaviour of Bryde's whales observed in our study seems to be associated to prey dynamics. Our data show that the study area is frequently used for foraging by this species in Brazilian waters.
ASYMPTOTICALLY OPTIMAL MULTI-ARMED BANDIT POLICIES UNDER A COST CONSTRAINT
Authors: Burnetas Apostolos , Kanavetas Odysseas , Katehakis Michael N.
Published: October 2016

We consider the multi-armed bandit problem under a cost constraint. Successive samples from each population are i.i.d. with unknown distribution and each sample incurs a known population-dependent cost. The objective is to design an adaptive sampling policy to maximize the expected sum ofnsamples such that the average cost does not exceed a given bound sample-path wise. We establish an asymptotic lower bound for the regret of feasible uniformly fast convergent policies, and construct a class of policies, which achieve the bound. We also provide their explicit form under Normal distributions with unknown means and known variances.
Barcelona beyond the Seas. A Catalan Enclave in Colonial Venezuela
Authors: Harwich Nikita
Published: October 2016

The town of Barcelona in Venezuela, with a present population of nearly half a million inhabitants, is – by far – the most important New World settlement bearing the name of Catalonia’s capital. It owes its name to its founder, Joan Orpí i del Pou, also known as Juan de Orpín or Urpín (Piera, 1593 – Barcelona, Venezuela, 1645), who managed to distinguish himself as one of the last conquistadors within the territory of present-day Venezuela. This was no easy task since a Catalan was, technically, not allowed to reside or even to travel to lands under the exclusive control of the Crown of Castille and León. However, since its foundation in 1638, Nueva Barcelona del Cerro Santo was soon to become a sort of Catalan enclave in eastern Venezuela, particularly due to the influence of the Catalan Capuchin missionaries who, since the end of the 17th century on, used it as a base for inland penetration. Similarly, Venezuela’s Barcelona was one of the important trading posts for the Compañía de Comercio de Barcelona, following the latter’s foundation in 1755. A sizeable community of Catalan merchants ensured the town’s growth and prosperity at the turn of the 19th century. This community also fuelled a strong resistance against the independence movement from 1810 onwards, as Barcelona was to become a savagely disputed prey between royalist and patriot armies: the episode of the Casa Fuerte massacre in 1817 is still today remembered as a landmark of royalist cruelty, even though the revenge later exerted by the patriot troops in no way fell behind in terms of mercilessness. The Catalans were particularly singled out and, with few exceptions, were all either killed or forced to leave.
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid
Authors: Wong Vanessa K. , Baker Stephen , Connor Thomas R. , Pickard Derek , Page Andrew J. , Dave Jayshree , Murphy Niamh , Holliman Richard , Sefton Armine , Millar Michael , Dyson Zoe A. , Dougan Gordon , Holt Kathryn E. ,   International Typhoid Consortium, Parkhill Julian , Feasey Nicholas A. , Kingsley Robert A. , Thomson Nicholas R. , Keane Jacqueline A. , Weill François- Xavier , Le Hello Simon , Hawkey Jane , Edwards David J. , Harris Simon R. , Cain Amy K. , Hadfield James , Hart Peter J. , Thieu Nga Tran Vu , Klemm Elizabeth J. , Breiman Robert F. , Watson Conall H. , Edmunds W. John , Kariuki Samuel , Gordon Melita A. , Heyderman Robert S. , Okoro Chinyere , Jacobs Jan , Lunguya Octavie , Msefula Chisomo , Chabalgoity Jose A. , Kama Mike , Jenkins Kylie , Dutta Shanta , Marks Florian , Campos Josefina , Thompson Corinne , Obaro Stephen , MacLennan Calman A. , Dolecek Christiane , Keddy Karen H. , Smith Anthony M. , Parry Christopher M. , Karkey Abhilasha , Dongol Sabina , Basnyat Buddha , Arjyal Amit , Mulholland E. Kim , Campbell James I. , Dufour Muriel , Bandaranayake Don , Toleafoa Take N. , Singh Shalini Pravin , Hatta Mochammad , Newton Paul N. , Dance David , Davong Viengmon , Onsare Robert S. , Isaia Lupeoletalalelei , Thwaites Guy , Wijedoru Lalith , Crump John A. , De Pinna Elizabeth , Nair Satheesh , Nilles Eric J. , Thanh Duy Pham , Turner Paul , Soeng Sona , Valcanis Mary , Powling Joan , Dimovski Karolina , Hogg Geoff , Farrar Jeremy , Mather Alison E. , Amos Ben
Published: October 2016

The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.
Environmental fatty acids enable emergence of infectious Staphylococcus aureus resistant to FASII-targeted antimicrobials
Authors: Morvan Claire , Halpern David , Kénanian Gérald , Hays Constantin , Anba-Mondoloni Jamila , Brinster Sophie , Kennedy Sean , Trieu-Cuot Patrick , Poyart Claire , Lamberet Gilles , Gloux Karine , Gruss Alexandra
Published: October 2016

The bacterial pathway for fatty acid biosynthesis, FASII, is a target for development of new anti-staphylococcal drugs. This strategy is based on previous reports indicating that self-synthesized fatty acids appear to be indispensable for Staphylococcus aureus growth and virulence, although other bacteria can use exogenous fatty acids to compensate FASII inhibition. Here we report that staphylococci can become resistant to the FASII-targeted inhibitor triclosan via high frequency mutations in fabD, one of the FASII genes. The fabD mutants can be conditional for FASII and not require exogenous fatty acids for normal growth, and can use diverse fatty acid combinations (including host fatty acids) when FASII is blocked. These mutants show cross-resistance to inhibitors of other FASII enzymes and are infectious in mice. Clinical isolates bearing fabD polymorphisms also bypass FASII inhibition. We propose that fatty acid-rich environments within the host, in the presence of FASII inhibitors, might favour the emergence of staphylococcal strains displaying resistance to multiple FASII inhibitors.
Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma
Authors: Zhao Ling-Hao , Liu Xiao , Yan He-Xin , Li Wei-Yang , Zeng Xi , Yang Yuan , Zhao Jie , Liu Shi-Ping , Zhuang Xue-Han , Lin Chuan , Qin Chen-Jie , Zhao Yi , Pan Ze-Ya , Huang Gang , Liu Hui , Zhang Jin , Wang Ruo-Yu , Yang Yun , Wen Wen , Lv Gui-Shuai , Zhang Hui-Lu , Wu Han , Huang Shuai , Wang Ming-Da , Tang Liang , Cao Hong-Zhi , Wang Ling , Lee Tin-Lap , Jiang Hui , Tan Ye-Xiong , Yuan Sheng-Xian , Hou Guo-Jun , Tao Qi-Fei , Xu Qin-Guo , Zhang Xiu-Qing , Wu Meng-Chao , Xu Xun , Wang Jun , Yang Huan-Ming , Zhou Wei-Ping , Wang Hong-Yang
Published: October 2016

Hepatitis B virus (HBV) can integrate into the human genome, contributing to genomic instability and hepatocarcinogenesis. Here by conducting high-throughput viral integration detection and RNA sequencing, we identify 4,225 HBV integration events in tumour and adjacent non-tumour samples from 426 patients with HCC. We show that HBV is prone to integrate into rare fragile sites and functional genomic regions including CpG islands. We observe a distinct pattern in the preferential sites of HBV integration between tumour and non-tumour tissues. HBV insertional sites are significantly enriched in the proximity of telomeres in tumours. Recurrent HBV target genes are identified with few that overlap. The overall HBV integration frequency is much higher in tumour genomes of males than in females, with a significant enrichment of integration into chromosome 17. Furthermore, a cirrhosis-dependent HBV integration pattern is observed, affecting distinct targeted genes. Our data suggest that HBV integration has a high potential to drive oncogenic transformation.
A cytosolic carbonic anhydrase molecular switch occurs in the gills of metamorphic sea lamprey
Authors: Ferreira-Martins D. , McCormick S. D. , Campos A. , Lopes-Marques M. , Osório H. , Coimbra J. , Castro L. F. C. , Wilson J. M.
Published: October 2016

Carbonic anhydrase plays a key role in CO2 transport, acid-base and ion regulation and metabolic processes in vertebrates. While several carbonic anhydrase isoforms have been identified in numerous vertebrate species, basal lineages such as the cyclostomes have remained largely unexamined. Here we investigate the repertoire of cytoplasmic carbonic anhydrases in the sea lamprey (Petromyzon marinus), that has a complex life history marked by a dramatic metamorphosis from a benthic filter-feeding ammocoete larvae into a parasitic juvenile which migrates from freshwater to seawater. We have identified a novel carbonic anhydrase gene (ca19) beyond the single carbonic anhydrase gene (ca18) that was known previously. Phylogenetic analysis and synteny studies suggest that both carbonic anhydrase genes form one or two independent gene lineages and are most likely duplicates retained uniquely in cyclostomes. Quantitative PCR of ca19 and ca18 and protein expression in gill across metamorphosis show that the ca19 levels are highest in ammocoetes and decrease during metamorphosis while ca18 shows the opposite pattern with the highest levels in post-metamorphic juveniles. We propose that a unique molecular switch occurs during lamprey metamorphosis resulting in distinct gill carbonic anhydrases reflecting the contrasting life modes and habitats of these life-history stages.
A key process controlling the wet removal of aerosols: new observational evidence
Authors: Ohata Sho , Moteki Nobuhiro , Mori Tatsuhiro , Koike Makoto , Kondo Yutaka
Published: October 2016

The lifetime and spatial distributions of accumulation-mode aerosols in a size range of approximately 0.05–1 μm and thus their global and regional climate impacts, are primarily constrained by their removal via cloud and precipitation (wet removal). However, the microphysical process that predominantly controls the removal efficiency remains unidentified because of observational difficulties. Here, we demonstrate that the activation of aerosols to cloud droplets (nucleation scavenging) predominantly controls the wet removal efficiency of accumulation-mode aerosols, using water-insoluble black carbon as an observable particle tracer during the removal process. From simultaneous ground-based observations of black carbon in air (prior to removal) and in rainwater (after removal) in Tokyo, Japan, we found that the wet removal efficiency depends strongly on particle size and the size dependence can be explained quantitatively by the observed size-dependent cloud-nucleating ability. Furthermore, our observational method provides an estimate of the effective supersaturation of water vapour in precipitating cloud clusters, a key parameter controlling nucleation scavenging. These novel data firmly indicate the importance of quantitative numerical simulations of the nucleation scavenging process to improve the model’s ability to predict the atmospheric aerosol burden and the resultant climate forcings and enable a new validation of such simulations.
The antenna of horse stomach bot flies: morphology and phylogenetic implications (Oestridae, Gasterophilinae: Gasterophilus Leach)
Authors: Zhang Dong , Li Xinyu , Liu Xianhui , Wang Qike , Pape Thomas
Published: October 2016

Antennae are among the most elaborate sensory organs in adult flies, and they provide rich information for phylogenic studies. The antennae of five out of eight species of Gasterophilus Leach (G. haemorrhoidalis (Linnaeus), G. intestinalis (De Geer), G. nasalis (Linnaeus), G. nigricornis (Loew) and G. pecorum (Fabricius)), were examined using scanning electron microscopy. The general morphology, including distribution, type, size, and ultrastructure of antennal sensilla were presented, and the definition of auriculate sensilla and sensory pits were updated and clarified. Eighteen antennal characters were selected to construct the first species-level phylogeny of this genus. The monophyly of Gasterophilus was supported by the presence of coeloconic sensilla III on the antennal arista. The species-level cladogram showed G. pecorum branching off at the base, and the remaining species forming the topology (G. intestinalis+ (G. haemorrhoidalis+ (G. nasalis+ G. nigricornis))). Our research shows the importance of the antennal ultrastructure as a reliable source for phylogenetic analysis.
Deficiency in Toll-interacting protein (Tollip) skews inflamed yet incompetent innate leukocytes in vivo during DSS-induced septic colitis
Authors: Diao Na , Zhang Yao , Chen Keqiang , Yuan Ruoxi , Lee Christina , Geng Shuo , Kowalski Elizabeth , Guo Wen , Xiong Huabao , Li Mingsong , Li Liwu
Published: October 2016

Functionally compromised neutrophils contribute to adverse clinical outcomes in patients with severe inflammation and injury such as colitis and sepsis. However, the ontogeny of dysfunctional neutrophil during septic colitis remain poorly understood. We report that the dysfunctional neutrophil may be derived by the suppression of Toll-interacting-protein (Tollip). We observed that Tollip deficient neutrophils had compromised migratory capacity toward bacterial product fMLF due to reduced activity of AKT and reduction of FPR2, reduced potential to generate bacterial-killing neutrophil extra-cellular trap (NET), and compromised bacterial killing activity. On the other hand, Tollip deficient neutrophils had elevated levels of CCR5, responsible for their homing to sterile inflamed tissues. The inflamed and incompetent neutrophil phenotype was also observed in vivo in Tollip deficient mice subjected to DSS-induced colitis. We observed that TUDCA, a compound capable of restoring Tollip cellular function, can potently alleviate the severity of DSS-induced colitis. In humans, we observed significantly reduced Tollip levels in peripheral blood collected from human colitis patients as compared to blood samples from healthy donors. Collectively, our data reveal a novel mechanism in Tollip alteration that underlies the inflamed and incompetent polarization of neutrophils leading to severe outcomes of colitis.
Directional and monochromatic thermal emitter from epsilon-near-zero conditions in semiconductor hyperbolic metamaterials
Authors: Campione Salvatore , Marquier Francois , Hugonin Jean-Paul , Ellis A. Robert , Klem John F. , Sinclair Michael B. , Luk Ting S.
Published: October 2016

The development of novel thermal sources that control the emission spectrum and the angular emission pattern is of fundamental importance. In this paper, we investigate the thermal emission properties of semiconductor hyperbolic metamaterials (SHMs). Our structure does not require the use of any periodic corrugation to provide monochromatic and directional emission properties. We show that these properties arise because of epsilon-near-zero conditions in SHMs. The thermal emission is dominated by the epsilon-near-zero effect in the doped quantum wells composing the SHM. Furthermore, different properties are observed for s and p polarizations, following the characteristics of the strong anisotropy of hyperbolic metamaterials.
Feature Subset Selection for Cancer Classification Using Weight Local Modularity
Authors: Zhao Guodong , Wu Yan
Published: October 2016

Microarray is recently becoming an important tool for profiling the global gene expression patterns of tissues. Gene selection is a popular technology for cancer classification that aims to identify a small number of informative genes from thousands of genes that may contribute to the occurrence of cancers to obtain a high predictive accuracy. This technique has been extensively studied in recent years. This study develops a novel feature selection (FS) method for gene subset selection by utilizing the Weight Local Modularity (WLM) in a complex network, called the WLMGS. In the proposed method, the discriminative power of gene subset is evaluated by using the weight local modularity of a weighted sample graph in the gene subset where the intra-class distance is small and the inter-class distance is large. A higher local modularity of the gene subset corresponds to a greater discriminative of the gene subset. With the use of forward search strategy, a more informative gene subset as a group can be selected for the classification process. Computational experiments show that the proposed algorithm can select a small subset of the predictive gene as a group while preserving classification accuracy.
Gallic acid prevents isoproterenol-induced cardiac hypertrophy and fibrosis through regulation of JNK2 signaling and Smad3 binding activity
Authors: Ryu Yuhee , Jin Li , Kee Hae Jin , Piao Zhe Hao , Cho Jae Yeong , Kim Gwi Ran , Choi Sin Young , Lin Ming Quan , Jeong Myung Ho
Published: October 2016

Gallic acid, a type of phenolic acid, has been shown to have beneficial effects in inflammation, vascular calcification, and metabolic diseases. The present study was aimed at determining the effect and regulatory mechanism of gallic acid in cardiac hypertrophy and fibrosis. Cardiac hypertrophy was induced by isoproterenol (ISP) in mice and primary neonatal cardiomyocytes. Gallic acid pretreatment attenuated concentric cardiac hypertrophy. It downregulated the expression of atrial natriuretic peptide, brain natriuretic peptide, and beta-myosin heavy chain in vivo and in vitro. Moreover, it prevented interstitial collagen deposition and expression of fibrosis-associated genes. Upregulation of collagen type I by Smad3 overexpression was observed in cardiac myoblast H9c2 cells but not in cardiac fibroblasts. Gallic acid reduced the DNA binding activity of phosphorylated Smad3 in Smad binding sites of collagen type I promoter in rat cardiac fibroblasts. Furthermore, it decreased the ISP-induced phosphorylation of c-Jun N-terminal kinase (JNK) and extracellular signal regulated kinase (ERK) protein in mice. JNK2 overexpression reduced collagen type I and Smad3 expression as well as GATA4 expression in H9c2 cells and cardiac fibroblasts. Gallic acid might be a novel therapeutic agent for the prevention of cardiac hypertrophy and fibrosis by regulating the JNK2 and Smad3 signaling pathway.
Tuning two-dimensional nanomaterials by intercalation: materials, properties and applications
Authors: Wan Jiayu , Lacey Steven D. , Dai Jiaqi , Bao Wenzhong , Fuhrer Michael S. , Hu Liangbing
Published: October 2016

2D materials have attracted tremendous attention due to their unique physical and chemical properties since the discovery of graphene. Among all modification methods, intercalation has emerged as a unique and powerful tool to further tune the properties of these atomically thin materials.
Discovery of a VHL and HIF1α interaction inhibitor with in vivo angiogenic activity via structure-based virtual screening
Authors: Yang Chao , Wang Wanhe , Chen Linmin , Liang Jiaxin , Lin Sheng , Lee Ming-Yuen , Ma Dik-Lung , Leung Chung-Hang
Published: October 2016

We describe herein compound 1, which is similar to many known natural products, as an inhibitor of the VHL–HIF1α interaction via structure-based virtual screening.
Multifaceted magnetization dynamics in the mononuclear complex [ReIVCl4(CN)2]2−
Authors: Feng Xiaowen , Liu Jun-Liang , Pedersen Kasper S. , Nehrkorn Joscha , Schnegg Alexander , Holldack Karsten , Bendix Jesper , Sigrist Marc , Mutka Hannu , Samohvalov Dumitru , Aguilà David , Tong Ming-Liang , Long Jeffrey R. , Clérac Rodolphe
Published: October 2016

Slow magnetization dynamics in [ReIVCl4(CN)2]2−occursviamultiple intricate relaxation processes.
A visible-light photocatalytic N-radical cascade of hydrazones for the synthesis of dihydropyrazole-fused benzosultams
Authors: Zhao Quan-Qing , Hu Xiao-Qiang , Yang Meng-Nan , Chen Jia-Rong , Xiao Wen-Jing
Published: October 2016

An efficient N-centred radical 5-exo cyclization/addition/aromatization cascade by cooperative visible light photoredox and cobalt catalysis is described, giving dihydropyrazole-fused benzosultams in satisfactory yields.
Quantitative and regiocontrolled cross-photocycloaddition of the anticancer drug 5-fluorouracil achieved in a cocrystal
Authors: Duncan Andrew J. E. , Dudovitz Roxanne L. , Dudovitz Shawna J. , Stojaković Jelena , Mariappan S. V. Santhana , MacGillivray Leonard R.
Published: October 2016

A cocrystal of the anticancer drug 5-fluorouracil and a bis(pyridyl)ethylene undergoes a quantitative cross-photocycloaddition.
Preparation and optical properties of Fe3O4 nanoparticles-doped blue phase liquid crystal
Authors: He Wan-Li , Zhang Wei-Kai , Xu Huan , Li Li-Hao , Yang Zhou , Cao Hui , Wang Dong , Zheng Zhi-Gang , Yang Huai
Published: October 2016

Magnetic Fe3O4 nanoparticle doped blue phase liquid crystal (BPLC) was successfully prepared and characterized. Interestingly, the Fe3O4 doped BPLC composite was found that had relatively strong contrast ratio in magnetic-addressed display performance than the composite in other phases.
Two-photon excitation nanoparticles for photodynamic therapy
Authors: Shen Yizhong , Shuhendler Adam J. , Ye Deju , Xu Jing-Juan , Chen Hong-Yuan
Published: October 2016

Integration of the two-photon excitation (TPE) technique and nanomaterials to construct TPE nanoparticle-based photosensitizers for PDT is summarized and reviewed.
Thermodynamics of biphasic lanthanide extraction by tripodal diglycolamide: a solution calorimetry study
Authors: Ansari Seraj A. , Mohapatra Prasanta K. , Verboom Willem , Rao Linfeng
Published: October 2016

Isothermal titration calorimetry has been used for the direct measurement of the enthalpy of extraction (ΔHextr) of metal ions in a solvent extraction process.
Spinning micropipette liquid emulsion generator for single cell whole genome amplification
Authors: Chen Zitian , Fu Yusi , Zhang Fangli , Liu Lu , Zhang Naiqing , Zhou Dong , Yang Junrui , Pang Yuhong , Huang Yanyi
Published: October 2016

The spinning micro-pipette liquid emulsion (SiMPLE) generator can produce highly stable monodisperse picoliter-size water-in-oil emulsions which can be integrated with conventional experimental operations.
KinView: a visual comparative sequence analysis tool for integrated kinome research
Authors: McSkimming Daniel Ian , Dastgheib Shima , Baffi Timothy R. , Byrne Dominic P. , Ferries Samantha , Scott Steven Thomas , Newton Alexandra C. , Eyers Claire E. , Kochut Krzysztof J. , Eyers Patrick A. , Kannan Natarajan
Published: October 2016

KinView enables both experts and novices to perform comparative analyses of cancer variants in the context of natural sequence variation and post-translational modifications across evolutionary groups of kinases.
An evolution-based DNA-binding residue predictor using a dynamic query-driven learning scheme
Authors: Chai H. , Zhang J. , Yang G. , Ma Z.
Published: October 2016

A dynamic query-driven learning scheme helps to make more use of proteins with known structure and functions.
Effect of novel triazole–amino acid hybrids on growth and virulence of Candida species: in vitro and in vivo studies
Authors: Aneja Babita , Irfan Mohammad , Kapil Charu , Jairajpuri Mohamad Aman , Maguire Ronan , Kavanagh Kevin , Rizvi M. Moshahid A. , Manzoor Nikhat , Azam Amir , Abid Mohammad
Published: October 2016

Twenty four triazole–amino acid hybrids have been designed and synthesized, among which compounds68and70exhibited most potentin vitroandin vivoanticandidal activity.
Enolate-mediated 1,3-dipolar cycloaddition reactions of allyl ketones with nitrile oxides: direct access to 3,5-disubstituted isoxazolines
Authors: Li Wenjun , Zhou Xiao , Shi Zhenyan , Liu Yang , Liu Zhantao , Gao Hua
Published: October 2016

TMG-catalyzed [3 + 2] organocatalytic 1,3-dipolar cycloaddition reactions of allyl ketones with in situ generated nitrile oxides have been developed. This strategy could generate 3,5-disubstituted isoxazolines in high yields and regioselectivities.
Synthesis and thermal properties of vinyl copolymers with phenyl vinylethylene carbonate and N-substituted maleimides undergoing color change with acid–base switching
Authors: Yoshida Yoshiaki , Endo Takeshi
Published: October 2016

The solution of P(PVEC-co-NMI), having an alternating structure, was a red color in basic solvents and the solution color changed with a high sensitively to acid–base switching.
The impact of zinc oxide nanoparticles on phosphorus removal and the microbial community in activated sludge in an SBR
Authors: Wang S. T. , Wang W. Q. , Zhang Z. R. , You H.
Published: October 2016

10 and 20 mg L−1 ZnO NPs damaged the integrity of cell membranes and the microbial community and affected phosphorus removal.
Electroless Ni–P plating on magnesium alloy by innovative, simple and non-toxic oxalate pretreatment and its corrosion protection
Authors: Seifzadeh D. , Kazemi Mohsenabadi H. , Rajabalizadeh Z.
Published: October 2016

The EDX analysis of the electroless Ni–P coating on 5 (a), 15 (b) and 30 (c) min, oxalate treatment time.
Physicochemical properties and biocompatibility of PZL/PLGA/bioglass composite scaffolds for bone tissue engineering
Authors: Cui Ning , Qian Junmin , Wang Jinlei , Wang Yaping , Xu Weijun , Wang Hongjie
Published: October 2016

Foamy poly(Nε-Cbz-l-lysine)/poly(lactic-co-glycolic acid)/bioglass composite scaffolds had appropriate physicochemical properties, good biomineralization ability, excellent cytocompatibility and histocompatibility, and desirable osteogenic ability.
Gate voltage-dependent magnetoresistance of Zn0.8Co0.2O:H
Authors: Cheon Miyeon , Cho Yong Chan , Cho Chae-Ryong , Park Chul Hong , Jeong Se-Young
Published: October 2016

The magnetoresistance (MR) of ZnCoO:H was measured at 7 K to verify the MR dependency on carrier density. It was found that MR increased with negative gate voltage. This increase in MR is not caused by an increase in pMR, but by a decrease in nMR.
Recent developments in the synthesis of condensed β-lactams
Authors: Kumar Yogesh , Singh Prabhpreet , Bhargava Gaurav
Published: October 2016

β-Lactams are important heterocycles with diverse pharmacological profiles and have emerged as useful organic synthons.