bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumour-initiating cell-specific miR-1246 and miR-1290 expression converge to promote non-small cell lung cancer progression
Authors: Zhang Wen Cai , Chin Tan Min , Yang Henry , Nga Min En , Lunny Declan Patrick , Lim Edwin Kok Hao , Sun Li Li , Pang Yin Huei , Leow Yi Ning , Malusay Shanneen Rossellini Y , Lim Priscilla Xin Hui , Lee Jeravan Zili , Tan Benedict Jian Wei , Shyh-Chang Ng , Lim Elaine Hsuen , Lim Wan Teck , Tan Daniel Shao Weng , Tan Eng Huat , Tai Bee Choo , Soo Ross Andrew , Tam Wai Leong , Lim Bing
Published: June 2016

The tumour-initiating cell (TIC) model accounts for phenotypic and functional heterogeneity among tumour cells. MicroRNAs (miRNAs) are regulatory molecules frequently aberrantly expressed in cancers, and may contribute towards tumour heterogeneity and TIC behaviour. More recent efforts have focused on miRNAs as diagnostic or therapeutic targets. Here, we identified the TIC-specific miRNAs, miR-1246 and miR-1290, as crucial drivers for tumour initiation and cancer progression in human non-small cell lung cancer. The loss of either miRNA impacted the tumour-initiating potential of TICs and their ability to metastasize. Longitudinal analyses of serum miR-1246 and miR-1290 levels across time correlate their circulating levels to the clinical response of lung cancer patients who were receiving ongoing anti-neoplastic therapies. Functionally, direct inhibition of either miRNA with locked nucleic acid administered systemically, can arrest the growth of established patient-derived xenograft tumours, thus indicating that these miRNAs are clinically useful as biomarkers for tracking disease progression and as therapeutic targets.
Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute
Authors: Miyoshi Tomohiro , Ito Kosuke , Murakami Ryo , Uchiumi Toshio
Published: June 2016

Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson–Crick base-pairing even in the 3′-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5′ base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region.
Uncertainty in soil data can outweigh climate impact signals in global crop yield simulations
Authors: Folberth Christian , Skalský Rastislav , Moltchanova Elena , Balkovič Juraj , Azevedo Ligia B. , Obersteiner Michael , van der Velde Marijn
Published: June 2016

Global gridded crop models (GGCMs) are increasingly used for agro-environmental assessments and estimates of climate change impacts on food production. Recently, the influence of climate data and weather variability on GGCM outcomes has come under detailed scrutiny, unlike the influence of soil data. Here we compare yield variability caused by the soil type selected for GGCM simulations to weather-induced yield variability. Without fertilizer application, soil-type-related yield variability generally outweighs the simulated inter-annual variability in yield due to weather. Increasing applications of fertilizer and irrigation reduce this variability until it is practically negligible. Importantly, estimated climate change effects on yield can be either negative or positive depending on the chosen soil type. Soils thus have the capacity to either buffer or amplify these impacts. Our findings call for improvements in soil data available for crop modelling and more explicit accounting for soil variability in GGCM simulations.
Coupling of Higgs and Leggett modes in non-equilibrium superconductors
Authors: Krull H. , Bittner N. , Uhrig G. S. , Manske D. , Schnyder A. P.
Published: June 2016

In equilibrium systems amplitude and phase collective modes are decoupled, as they are mutually orthogonal excitations. The direct detection of these Higgs and Leggett collective modes by linear-response measurements is not possible, because they do not couple directly to the electromagnetic field. In this work, using numerical exact simulations we show for the case of two-gap superconductors, that optical pump–probe experiments excite both Higgs and Leggett modes out of equilibrium. We find that this non-adiabatic excitation process introduces a strong interaction between the collective modes, which is absent in equilibrium. Moreover, we propose a type of pump–probe experiment, which allows to probe and coherently control the Higgs and Leggett modes, and thus the order parameter directly. These findings go beyond two-band superconductors and apply to general collective modes in quantum materials.
Ultrasensitive photodetectors exploiting electrostatic trapping and percolation transport
Authors: Zhang Yingjie , Hellebusch Daniel J. , Bronstein Noah D. , Ko Changhyun , Ogletree D. Frank , Salmeron Miquel , Alivisatos A. Paul
Published: June 2016

The sensitivity of semiconductor photodetectors is limited by photocarrier recombination during the carrier transport process. We developed a new photoactive material that reduces recombination by physically separating hole and electron charge carriers. This material has a specific detectivity (the ability to detect small signals) of 5 × 1017 Jones, the highest reported in visible and infrared detectors at room temperature, and 4–5 orders of magnitude higher than that of commercial single-crystal silicon detectors. The material was fabricated by sintering chloride-capped CdTe nanocrystals into polycrystalline films, where Cl selectively segregates into grain boundaries acting as n-type dopants. Photogenerated electrons concentrate in and percolate along the grain boundaries—a network of energy valleys, while holes are confined in the grain interiors. This electrostatic field-assisted carrier separation and percolation mechanism enables an unprecedented photoconductive gain of 1010e− per photon, and allows for effective control of the device response speed by active carrier quenching.
Activation of STING requires palmitoylation at the Golgi
Authors: Mukai Kojiro , Konno Hiroyasu , Akiba Tatsuya , Uemura Takefumi , Waguri Satoshi , Kobayashi Toshihide , Barber Glen N. , Arai Hiroyuki , Taguchi Tomohiko
Published: June 2016

Stimulator of interferon genes (STING) is essential for the type I interferon response against DNA pathogens. In response to the presence of DNA and/or cyclic dinucleotides, STING translocates from the endoplasmic reticulum to perinuclear compartments. However, the role of this subcellular translocation remains poorly defined. Here we show that palmitoylation of STING at the Golgi is essential for activation of STING. Treatment with palmitoylation inhibitor 2-bromopalmitate (2-BP) suppresses palmitoylation of STING and abolishes the type I interferon response. Mutation of two membrane-proximal Cys residues (Cys88/91) suppresses palmitoylation, and this STING mutant cannot induce STING-dependent host defense genes. STING variants that constitutively induce the type I interferon response were found in patients with autoimmune diseases. The response elicited by these STING variants is effectively inhibited by 2-BP or an introduction of Cys88/91Ser mutation. Our results may lead to new treatments for cytosolic DNA-triggered autoinflammatory diseases.
A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis
Authors: Liu Yanfeng , Link Hannes , Liu Long , Du Guocheng , Chen Jian , Sauer Uwe
Published: June 2016

Recent advances in genome engineering have further widened the gap between our ability to implement essentially any genetic change and understanding the impact of these changes on cellular function. We lack efficient methods to diagnose limiting steps in engineered pathways. Here, we develop a generally applicable approach to reveal limiting steps within a synthetic pathway. It is based on monitoring metabolite dynamics and simplified kinetic modelling to differentiate between putative causes of limiting product synthesis during the start-up phase of the pathway with near-maximal rates. We examine the synthetic N-acetylglucosamine (GlcNAc) pathway in Bacillus subtilis and find none of the acetyl-, amine- or glucose-moiety precursors to limit synthesis. Our dynamic metabolomics approach predicts an energy-dissipating futile cycle between GlcNAc6P and GlcNAc as the primary problem in the pathway. Deletion of the responsible glucokinase more than doubles GlcNAc productivity by restoring healthy growth of the overproducing strain.
Faecal bile acids are natural ligands of the mouse accessory olfactory system
Authors: Doyle Wayne I. , Dinser Jordan A. , Cansler Hillary L. , Zhang Xingjian , Dinh Daniel D. , Browder Natasha S. , Riddington Ian M. , Meeks Julian P.
Published: June 2016

The accessory olfactory system (AOS) guides behaviours that are important for survival and reproduction, but understanding of AOS function is limited by a lack of identified natural ligands. Here we report that mouse faeces are a robust source of AOS chemosignals and identify bile acids as a class of natural AOS ligands. Single-unit electrophysiological recordings from accessory olfactory bulb neurons in ex vivo preparations show that AOS neurons are strongly and selectively activated by peripheral stimulation with mouse faecal extracts. Faecal extracts contain several unconjugated bile acids that cause concentration-dependent neuronal activity in the AOS. Many AOS neurons respond selectively to bile acids that are variably excreted in male and female mouse faeces, and others respond to bile acids absent in mouse faeces. These results identify faeces as a natural source of AOS information, and suggest that bile acids may be mammalian pheromones and kairomones.
Unassisted photoelectrochemical water splitting exceeding 7% solar-to-hydrogen conversion efficiency using photon recycling
Authors: Shi Xinjian , Jeong Hokyeong , Oh Seung Jae , Ma Ming , Zhang Kan , Kwon Jeong , Choi In Taek , Choi Il Yong , Kim Hwan Kyu , Kim Jong Kyu , Park Jong Hyeok
Published: June 2016

Various tandem cell configurations have been reported for highly efficient and spontaneous hydrogen production from photoelectrochemical solar water splitting. However, there is a contradiction between two main requirements of a front photoelectrode in a tandem cell configuration, namely, high transparency and high photocurrent density. Here we demonstrate a simple yet highly effective method to overcome this contradiction by incorporating a hybrid conductive distributed Bragg reflector on the back side of the transparent conducting substrate for the front photoelectrochemical electrode, which functions as both an optical filter and a conductive counter-electrode of the rear dye-sensitized solar cell. The hybrid conductive distributed Bragg reflectors were designed to be transparent to the long-wavelength part of the incident solar spectrum (λ>500 nm) for the rear solar cell, while reflecting the short-wavelength photons (λ<500 nm) which can then be absorbed by the front photoelectrochemical electrode for enhanced photocurrent generation.
Slower carriers limit charge generation in organic semiconductor light-harvesting systems
Authors: Stolterfoht Martin , Armin Ardalan , Shoaee Safa , Kassal Ivan , Burn Paul , Meredith Paul
Published: June 2016

Blends of electron-donating and -accepting organic semiconductors are widely used as photoactive materials in next-generation solar cells and photodetectors. The yield of free charges in these systems is often determined by the separation of interfacial electron–hole pairs, which is expected to depend on the ability of the faster carrier to escape the Coulomb potential. Here we show, by measuring geminate and non-geminate losses and key transport parameters in a series of bulk-heterojunction solar cells, that the charge-generation yield increases with increasing slower carrier mobility. This is in direct contrast with the well-established Braun model where the dissociation rate is proportional to the mobility sum, and recent models that underscore the importance of fullerene aggregation for coherent electron propagation. The behaviour is attributed to the restriction of opposite charges to different phases, and to an entropic contribution that favours the joint separation of both charge carriers.
Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription
Authors: Ramakrishnan Saravanan , Pokhrel Srijana , Palani Sowmiya , Pflueger Christian , Parnell Timothy J. , Cairns Bradley R. , Bhaskara Srividya , Chandrasekharan Mahesh B.
Published: June 2016

Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic roles in transcription and chromatin dynamics remain poorly understood. We investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Here, we show that Set1 and Jhd2 predominantly co-regulate genome-wide transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal turnover and occupancy during transcriptional co-regulation. Moreover, we find a genome-wide co-regulation of chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study puts forth a model wherein combined actions of Set1 and Jhd2 via modulating H3K4 methylation−demethylation together control chromatin dynamics during various facets of transcriptional regulation.
Discovery of earth-abundant nitride semiconductors by computational screening and high-pressure synthesis
Authors: Hinuma Yoyo , Hatakeyama Taisuke , Kumagai Yu , Burton Lee A. , Sato Hikaru , Muraba Yoshinori , Iimura Soshi , Hiramatsu Hidenori , Tanaka Isao , Hosono Hideo , Oba Fumiyasu
Published: June 2016

Nitride semiconductors are attractive because they can be environmentally benign, comprised of abundant elements and possess favourable electronic properties. However, those currently commercialized are mostly limited to gallium nitride and its alloys, despite the rich composition space of nitrides. Here we report the screening of ternary zinc nitride semiconductors using first-principles calculations of electronic structure, stability and dopability. This approach identifies as-yet-unreported CaZn2N2 that has earth-abundant components, smaller carrier effective masses than gallium nitride and a tunable direct bandgap suited for light emission and harvesting. High-pressure synthesis realizes this phase, verifying the predicted crystal structure and band-edge red photoluminescence. In total, we propose 21 promising systems, including Ca2ZnN2, Ba2ZnN2 and Zn2PN3, which have not been reported as semiconductors previously. Given the variety in bandgaps of the identified compounds, the present study expands the potential suitability of nitride semiconductors for a broader range of electronic, optoelectronic and photovoltaic applications.
Mnemonic convergence in the human hippocampus
Authors: Backus Alexander R. , Bosch Sander E. , Ekman Matthias , Grabovetsky Alejandro Vicente , Doeller Christian F.
Published: June 2016

The ability to form associations between a multitude of events is the hallmark of episodic memory. Computational models have espoused the importance of the hippocampus as convergence zone, binding different aspects of an episode into a coherent representation, by integrating information from multiple brain regions. However, evidence for this long-held hypothesis is limited, since previous work has largely focused on representational and network properties of the hippocampus in isolation. Here we identify the hippocampus as mnemonic convergence zone, using a combination of multivariate pattern and graph-theoretical network analyses of functional magnetic resonance imaging data from humans performing an associative memory task. We observe overlap of conjunctive coding and hub-like network attributes in the hippocampus. These results provide evidence for mnemonic convergence in the hippocampus, underlying the integration of distributed information into episodic memory representations.
Thermoelectric materials by using two-dimensional materials with negative correlation between electrical and thermal conductivity
Authors: Lee Myoung-Jae , Ahn Ji-Hoon , Sung Ji Ho , Heo Hoseok , Jeon Seong Gi , Lee Woo , Song Jae Yong , Hong Ki-Ha , Choi Byeongdae , Lee Sung-Hoon , Jo Moon-Ho
Published: June 2016

In general, in thermoelectric materials the electrical conductivity σ and thermal conductivity κ are related and thus cannot be controlled independently. Previously, to maximize the thermoelectric figure of merit in state-of-the-art materials, differences in relative scaling between σ and κ as dimensions are reduced to approach the nanoscale were utilized. Here we present an approach to thermoelectric materials using tin disulfide, SnS2, nanosheets that demonstrated a negative correlation between σ and κ. In other words, as the thickness of SnS2 decreased, σ increased whereas κ decreased. This approach leads to a thermoelectric figure of merit increase to 0.13 at 300 K, a factor ∼1,000 times greater than previously reported bulk single-crystal SnS2. The Seebeck coefficient obtained for our two-dimensional SnS2 nanosheets was 34.7 mV K−1 for 16-nm-thick samples at 300 K.
A lake data set for the Tibetan Plateau from the 1960s, 2005, and 2014
Authors: Wan Wei , Long Di , Hong Yang , Ma Yingzhao , Yuan Yuan , Xiao Pengfeng , Duan Hongtao , Han Zhongying , Gu Xingfa
Published: June 2016

Long-term datasets of number and size of lakes over the Tibetan Plateau (TP) are among the most critical components for better understanding the interactions among the cryosphere, hydrosphere, and atmosphere at regional and global scales. Due to the harsh environment and the scarcity of data over the TP, data accumulation and sharing become more valuable for scientists worldwide to make new discoveries in this region. This paper, for the first time, presents a comprehensive and freely available data set of lakes’ status (name, location, shape, area, perimeter, etc.) over the TP region dating back to the 1960s, including three time series, i.e., the 1960s, 2005, and 2014, derived from ground survey (the 1960s) or high-spatial-resolution satellite images from the China-Brazil Earth Resources Satellite (CBERS) (2005) and China’s newly launched GaoFen-1 (GF-1, which means high-resolution images in Chinese) satellite (2014). The data set could provide scientists with useful information for revealing environmental changes and mechanisms over the TP region.

Design Type(s)
time series design • observation design • data integration objective

Measurement Type(s)
lake topography

Technology Type(s)
remote sensing

Factor Type(s)

Sample Characteristic(s)
Tibetan Plateau • Qaidam Basin • Amu Darya • Brahmaputra River • River Ganges • Hexi District • Indus River • Mekong River • Salween River • Tarim Basin • Yangtze River • Yellow River • endorheic lake • exorheic lake

Machine-accessible metadata file describing the reported data (ISA-Tab format)
A database of marine phytoplankton abundance, biomass and species composition in Australian waters
Authors: Davies Claire H. , Coughlan Alex , Hallegraeff Gustaaf , Ajani Penelope , Armbrecht Linda , Atkins Natalia , Bonham Prudence , Brett Steve , Brinkman Richard , Burford Michele , Clementson Lesley , Coad Peter , Coman Frank , Davies Diana , Dela-Cruz Jocelyn , Devlin Michelle , Edgar Steven , Eriksen Ruth , Furnas Miles , Hassler Christel , Hill David , Holmes Michael , Ingleton Tim , Jameson Ian , Leterme Sophie C. , Lønborg Christian , McLaughlin James , McEnnulty Felicity , McKinnon A. David , Miller Margaret , Murray Shauna , Nayar Sasi , Patten Renee , Pausina Sarah A. , Pritchard Tim , Proctor Roger , Purcell-Meyerink Diane , Raes Eric , Rissik David , Ruszczyk Jason , Slotwinski Anita , Swadling Kerrie M. , Tattersall Katherine , Thompson Peter , Thomson Paul , Tonks Mark , Trull Thomas W. , Uribe-Palomino Julian , Waite Anya M. , Yauwenas Rouna , Zammit Anthony , Richardson Anthony J.
Published: June 2016

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels.
A protocol to convert spatial polyline data to network formats and applications to world urban road networks
Authors: Karduni Alireza , Kermanshah Amirhassan , Derrible Sybil
Published: June 2016

The study of geographical systems as graphs, and networks has gained significant momentum in the academic literature as these systems possess measurable and relevant network properties. Crowd-based sources of data such as OpenStreetMaps (OSM) have created a wealth of worldwide geographic information including on transportation systems (e.g., road networks). In this work, we offer a Geographic Information Systems (GIS) protocol to transfer polyline data into a workable network format in the form of; a node layer, an edge layer, and a list of nodes/edges with relevant geographic information (e.g., length). Moreover, we have developed an ArcGIS tool to perform this protocol on OSM data, which we have applied to 80 urban areas in the world and made the results freely available. The tool accounts for crossover roads such as ramps and bridges. A separate tool is also made available for planar data and can be applied to any line features in ArcGIS.
Biocontrol of the oriental armyworm, Mythimna separata, by the tachinid fly Exorista civilis is synergized by Cry1Ab protoxin
Authors: Jiang Xingfu , Zhang Lei , Yang Haixia , Sappington Thomas W. , Cheng Yunxia , Luo Li zhi
Published: June 2016

Tritrophic interactions between Mythimna separata, its tachinid parasite Exorista civilis and the Cry1Ab were examined. Although 6th instar M. separata mortality increased with increasing Cry1Ab concentration, some tolerance was evident. Likewise, parasitization by E. civilis resulted in only 18% host mortality. However, combination of Cry1Ab and E. civilis parasitization resulted in a significant Cry1Ab dose-dependent increase in mortality over that of either alone, including a 50–56% synergistic increase in efficacy at the two concentrations tested. Pupal weight, adult emergence and lifetime fecundity of M. separata derived from larvae surviving both agents were negatively affected. The ability of E. civilis to parasitize and subsequently develop on the host was not adversely influenced by Cry1Ab. Instead, pupation rate increased significantly among host larvae fed 3.125 μg/g Cry1Ab diet. Overall, our results demonstrate that use of Cry1Ab to control M. separata not only is compatible with the use of the tachinid parasitoid, but that the two methods can act synergistically to manage this destructive pest, provide support for the safety of transgenic Cry1Ab Bt plants in China. This example of two independent pest management strategies acting synergistically against a difficult pest offers a new perspective of broad significance in striving for agricultural sustainability.
The polysialic acid mimetics 5-nonyloxytryptamine and vinorelbine facilitate nervous system repair
Authors: Saini Vedangana , Lutz David , Kataria Hardeep , Kaur Gurcharan , Schachner Melitta , Loers Gabriele
Published: June 2016

Polysialic acid (PSA) is a large negatively charged glycan mainly attached to the neural cell adhesion molecule (NCAM). Several studies have shown that it is important for correct formation of brain circuitries during development and for synaptic plasticity, learning and memory in the adult. PSA also plays a major role in nervous system regeneration following injury. As a next step for clinical translation of PSA based therapeutics, we have previously identified the small organic compounds 5-nonyloxytryptamine and vinorelbine as PSA mimetics. Activity of 5-nonyloxytryptamine and vinorelbine had been confirmed in assays with neural cells from the central and peripheral nervous system in vitro and shown to be independent of their function as serotonin receptor 5-HT1B/1D agonist or cytostatic drug, respectively. As we show here in an in vivo paradigm for spinal cord injury in mice, 5-nonyloxytryptamine and vinorelbine enhance regain of motor functions, axonal regrowth, motor neuron survival and remyelination. These data indicate that 5-nonyloxytryptamine and vinorelbine may be re-tasked from their current usage as a 5-HT1B/1D agonist or cytostatic drug to act as mimetics for PSA to stimulate regeneration after injury in the mammalian nervous system.
Efficient generation of transgenic cattle using the DNA transposon and their analysis by next-generation sequencing
Authors: Yum Soo-Young , Lee Song-Jeon , Kim Hyun-Min , Choi Woo-Jae , Park Ji-Hyun , Lee Won-Wu , Kim Hee-Soo , Kim Hyeong-Jong , Bae Seong-Hun , Lee Je-Hyeong , Moon Joo-Yeong , Lee Ji-Hyun , Lee Choong-Il , Son Bong-Jun , Song Sang-Hoon , Ji Su-Min , Kim Seong-Jin , Jang Goo
Published: June 2016

Here, we efficiently generated transgenic cattle using two transposon systems (Sleeping Beauty and Piggybac) and their genomes were analyzed by next-generation sequencing (NGS). Blastocysts derived from microinjection of DNA transposons were selected and transferred into recipient cows. Nine transgenic cattle have been generated and grown-up to date without any health issues except two. Some of them expressed strong fluorescence and the transgene in the oocytes from a superovulating one were detected by PCR and sequencing. To investigate genomic variants by the transgene transposition, whole genomic DNA were analyzed by NGS. We found that preferred transposable integration (TA or TTAA) was identified in their genome. Even though multi-copies (i.e. fifteen) were confirmed, there was no significant difference in genome instabilities. In conclusion, we demonstrated that transgenic cattle using the DNA transposon system could be efficiently generated, and all those animals could be a valuable resource for agriculture and veterinary science.
Factors influencing immunologic response to hepatitis B vaccine in adults
Authors: Yang Shigui , Tian Guo , Cui Yuanxia , Ding Cheng , Deng Min , Yu Chengbo , Xu Kaijin , Ren Jingjing , Yao Jun , Li Yiping , Cao Qing , Chen Ping , Xie Tiansheng , Wang Chencheng , Wang Bing , Mao Chen , Ruan Bing , Jiang Tian’an , Li Lanjuan
Published: June 2016

Hepatitis B was still a worldwide health problem. This study aimed to conducted a systematic review and meta-analysis to assess a more precise estimation of factors that influence the response to hepatitis B vaccine in adults. Our included studies examined seroprotection rates close to the end of vaccination schedules in healthy adult populations. This meta-analysis including 21053 adults in 37 articles showed that a significantly decreased response to hepatitis B vaccine appeared in adults (age ≥ 40) (RR:1.86, 95% CI:1.55–2.23), male adults (RR:1.40, 95% CI:1.22–1.61), BMI ≥ 25 adults (RR:1.56, 95% CI:1.12–2.17), smoker (RR:1.53, 95% CI:1.21–1.93), and adults with concomitant disease (RR:1.39, 95% CI:1.04–1.86). Meanwhile, we further found a decreased response to hepatitis B vaccine appeared in adults (age ≥ 30) (RR:1.77, 95% CI:1.48–2.10), and adults (age ≥ 60) (RR:1.30, 95% CI:1.01–1.68). However, there were no difference in response to hepatitis B vaccine both in alcoholic (RR:0.90, 95% CI:0.64–1.26) and 0-1-12 vs. 0-1-6 vaccination schedule (RR:1.39, 95% CI:0.41–4.67). Pooling of these studies recommended the sooner the better for adult hepatitis B vaccine strategy. More vaccine doses, supplemental/additional strengthening immunity should be emphasized on the susceptible population of increasing aged, male, BMI ≥ 25, smoking and concomitant disease. The conventional 0-1-6 vaccination schedule could be still worth to be recommended.
Optimizing the robustness of electrical power systems against cascading failures
Authors: Zhang Yingrui , Yağan Osman
Published: June 2016

Electrical power systems are one of the most important infrastructures that support our society. However, their vulnerabilities have raised great concern recently due to several large-scale blackouts around the world. In this paper, we investigate the robustness of power systems against cascading failures initiated by a random attack. This is done under a simple yet useful model based on global and equal redistribution of load upon failures. We provide a comprehensive understanding of system robustness under this model by (i) deriving an expression for the final system size as a function of the size of initial attacks; (ii) deriving the critical attack size after which system breaks down completely; (iii) showing that complete system breakdown takes place through a first-order (i.e., discontinuous) transition in terms of the attack size; and (iv) establishing the optimal load-capacity distribution that maximizes robustness. In particular, we show that robustness is maximized when the difference between the capacity and initial load is the same for all lines; i.e., when all lines have the same redundant space regardless of their initial load. This is in contrast with the intuitive and commonly used setting where capacity of a line is a fixed factor of its initial load.
A Simplified Direct Lipid Mixing Lipoplex Preparation: Comparison of Liposomal-, Dimethylsulfoxide-, and Ethanol-Based Methods
Authors: Meisel Joseph W. , Gokel George W.
Published: June 2016

Established transfection methodology often uses commercial reagents, which must be formed into liposomes in a sequence of about half a dozen steps. The simplified method reported here is a direct lipid mixing approach that requires fewer steps, less manipulation, and is less time-consuming. Results are comparable to those obtained with more commonly used methods, as judged by a variety of analytical techniques and by comparisons of transfection results. The method reported here may be applied to non-liposome-forming compounds, thereby greatly expanding the range of structures that can be tested for transfection ability.
Improvement of the reverse tetracycline transactivator by single amino acid substitutions that reduce leaky target gene expression to undetectable levels
Authors: Roney Ian J. , Rudner Adam D. , Couture Jean-François , Kærn Mads
Published: June 2016

Conditional gene expression systems that enable inducible and reversible transcriptional control are essential research tools and have broad applications in biomedicine and biotechnology. The reverse tetracycline transcriptional activator is a canonical system for engineered gene expression control that enables graded and gratuitous modulation of target gene transcription in eukaryotes from yeast to human cell lines and transgenic animals. However, the system has a tendency to activate transcription even in the absence of tetracycline and this leaky target gene expression impedes its use. Here, we identify single amino-acid substitutions that greatly enhance the dynamic range of the system in yeast by reducing leaky transcription to undetectable levels while retaining high expression capacity in the presence of inducer. While the mutations increase the inducer concentration required for full induction, additional sensitivity-enhancing mutations can compensate for this effect and confer a high degree of robustness to the system. The novel transactivator variants will be useful in applications where tight and tunable regulation of gene expression is paramount.
The embryological basis of subclinical hypertrophic cardiomyopathy
Authors: Captur Gabriella , Ho Carolyn Y. , Schlossarek Saskia , Kerwin Janet , Mirabel Mariana , Wilson Robert , Rosmini Stefania , Obianyo Chinwe , Reant Patricia , Bassett Paul , Cook Andrew C. , Lindsay Susan , McKenna William J. , Mills Kevin , Elliott Perry M. , Mohun Timothy J. , Carrier Lucie , Moon James C.
Published: June 2016

Hypertrophic cardiomyopathy (HCM) is caused by mutations in sarcomeric proteins, the commonest being MYBPC3 encoding myosin-binding protein C. It is characterised by left ventricular hypertrophy but there is an important pre-hypertrophic phenotype with features including crypts, abnormal mitral leaflets and trabeculae. We investigated these during mouse cardiac development using high-resolution episcopic microscopy. In embryonic hearts from wildtype, homozygous (HO) and heterozygous (HET) Mybpc3-targeted knock-out (KO) mice we show that crypts (one or two) are a normal part of wildtype development but they almost all resolve by birth. By contrast, HO and HET embryos had increased crypt presence, abnormal mitral valve formation and alterations in the compaction process. In scarce normal human embryos, crypts were sometimes present. This study shows that features of the human pre-hypertrophic HCM phenotype occur in the mouse. In an animal model we demonstrate that there is an embryological HCM phenotype. Crypts are a normal part of cardiac development but, along with the mitral valve and trabeculae, their developmental trajectory is altered by the presence of HCM truncating Mybpc3 gene mutation.
Real world ocean rogue waves explained without the modulational instability
Authors: Fedele Francesco , Brennan Joseph , Ponce de León Sonia , Dudley John , Dias Frédéric
Published: June 2016

Since the 1990s, the modulational instability has commonly been used to explain the occurrence of rogue waves that appear from nowhere in the open ocean. However, the importance of this instability in the context of ocean waves is not well established. This mechanism has been successfully studied in laboratory experiments and in mathematical studies, but there is no consensus on what actually takes place in the ocean. In this work, we question the oceanic relevance of this paradigm. In particular, we analyze several sets of field data in various European locations with various tools and find that the main generation mechanism for rogue waves is the constructive interference of elementary waves enhanced by second-order bound nonlinearities and not the modulational instability. This implies that rogue waves are likely to be rare occurrences of weakly nonlinear random seas.
Brain hemodynamic activity during viewing and re-viewing of comedy movies explained by experienced humor
Authors: Jääskeläinen Iiro P. , Pajula Juha , Tohka Jussi , Lee Hsin-Ju , Kuo Wen-Jui , Lin Fa-Hsuan
Published: June 2016

Humor is crucial in human social interactions. To study the underlying neural processes, three comedy clips were shown twice to 20 volunteers during functional magnetic resonance imaging (fMRI). Inter-subject similarities in humor ratings, obtained immediately after fMRI, explained inter-subject correlation of hemodynamic activity in right frontal pole and in a number of other brain regions. General linear model analysis also indicated activity in right frontal pole, as well as in additional cortical areas and subcortically in striatum, explained by humorousness. The association of the right frontal pole with experienced humorousness is a novel finding, which might be related to humor unfolding over longer time scales in the movie clips. Specifically, frontal pole has been shown to exhibit longer temporal receptive windows than, e.g., sensory areas, which might have enabled processing of humor in the clips based on holding information and reinterpreting that in light of new information several (even tens of) seconds later. As another novel finding, medial and lateral prefrontal areas, frontal pole, posterior-inferior temporal areas, posterior parietal areas, posterior cingulate, striatal structures and amygdala showed reduced activity upon re-viewing of the clips, suggesting involvement in processing of humor related to novelty of the comedic events.
Ocean acidification reduces transfer of essential biomolecules in a natural plankton community
Authors: Bermúdez J. Rafael , Riebesell Ulf , Larsen Aud , Winder Monika
Published: June 2016

Ocean acidification (OA), a process of increasing seawater acidity caused by the uptake of anthropogenic carbon dioxide (CO2) by the ocean, is expected to change surface ocean pH to levels unprecedented for millions of years, affecting marine food web structures and trophic interactions. Using an in situ mesocosm approach we investigated effects of OA on community composition and trophic transfer of essential fatty acids (FA) in a natural plankton assemblage. Elevated pCO2 favored the smallest phytoplankton size class in terms of biomass, primarily picoeukaryotes, at the expense of chlorophyta and haptophyta in the nano-plankton size range. This shift in community composition and size structure was accompanied by a decline in the proportion of polyunsaturated FA (PUFA) to total FA content in the nano- and picophytoplankton size fractions. This decline was mirrored in a continuing reduction in the relative PUFA content of the dominant copepod, Calanus finmarchicus, which primarily fed on the nano-size class. Our results demonstrate that a shift in phytoplankton community composition and biochemical composition in response to rising CO2 can affect the transfer of essential compounds to higher trophic levels, which rely on their prey as a source for essential macromolecules.
Malaria transmission potential could be reduced with current and future climate change
Authors: Murdock C. C. , Sternberg E. D. , Thomas M. B.
Published: June 2016

Several studies suggest the potential for climate change to increase malaria incidence in cooler, marginal transmission environments. However, the effect of increasing temperature in warmer regions where conditions currently support endemic transmission has received less attention. We investigate how increases in temperature from optimal conditions (27 °C to 30 °C and 33 °C) interact with realistic diurnal temperature ranges (DTR: ± 0 °C, 3 °C and 4.5 °C) to affect the ability of key vector species from Africa and Asia (Anopheles gambiae and An. stephensi) to transmit the human malaria parasite, Plasmodium falciparum. The effects of increasing temperature and DTR on parasite prevalence, parasite intensity and mosquito mortality decreased overall vectorial capacity for both mosquito species. Increases of 3 °C from 27 °C reduced vectorial capacity by 51–89% depending on species and DTR, with increases in DTR alone potentially halving transmission. At 33 °C, transmission potential was further reduced for An. stephensi and blocked completely in An. gambiae. These results suggest that small shifts in temperature could play a substantial role in malaria transmission dynamics, yet few empirical or modeling studies consider such effects. They further suggest that rather than increase risk, current and future warming could reduce transmission potential in existing high transmission settings.
Non-homologous end joining repair in Xenopus egg extract
Authors: Zhu Songli , Peng Aimin
Published: June 2016

Non-homologous end joining (NHEJ) is a major DNA double-strand break (DSB) repair mechanism. We characterized here a series of plasmid-based DSB templates that were repaired in Xenopus egg extracts via the canonical, Ku-dependent NHEJ pathway. We showed that the template with compatible ends was efficiently repaired without end processing, in a manner that required the kinase activity of DNA-PKcs but not ATM. Moreover, non-compatible ends with blunt/3′-overhang, blunt/5′-overhang and 3′-overhang/5′-overhang were predominantly repaired with fill-in and ligation without the removal of end nucleotides. In contrast, 3′-overhang/3′-overhang and 5′-overhang/5′-overhang templates were processed by resection of 3–5 bases and fill-in of 1–4 bases prior to end ligation. Therefore, the NHEJ machinery exhibited a strong preference for precise repair; the presence of neither non-compatible ends nor protruding single strand DNA sufficiently warranted the action of nucleases. ATM was required for the efficient repair of all non-compatible ends including those repaired without end processing by nucleases, suggesting its role beyond phosphorylation and regulation of Artemis. Finally, dephosphorylation of the 5′-overhang/3′-overhang template reduced the efficiency of DNA repair without increasing the risk of end resection, indicating that end protection via prompt end ligation is not the sole mechanism that suppresses the action of nucleases.
Quantum chemistry and charge transport in biomolecules with superconducting circuits
Authors: García-Álvarez L. , Las Heras U. , Mezzacapo A. , Sanz M. , Solano E. , Lamata L.
Published: June 2016

We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects.
Effect of experimental laser imperfections on laser wakefield acceleration and betatron source
Authors: Ferri J. , Davoine X. , Fourmaux S. , Kieffer J. C. , Corde S. , Ta Phuoc K. , Lifschitz A.
Published: June 2016

Laser pulses in current ultra-short TW systems are far from being ideal Gaussian beams. The influence of the presence of non-Gaussian features of the laser pulse is investigated here from experiments and 3D Particle-in-Cell simulations. Both the experimental intensity distribution and wavefront are used as input in the simulations. It is shown that a quantitative agreement between experimental data and simulations requires to use realistic pulse features. Moreover, some trends found in the experiments, such as the growing of the X-ray signal with the plasma length, can only be retrieved in simulations with realistic pulses. The performances on the electron acceleration and the synchrotron X-ray emission are strongly degraded by these non-Gaussian features, even keeping constant the total laser energy. A drop on the X-ray photon number by one order of magnitude was found. This clearly put forward the limitation of using a Gaussian beam in the simulations.
Pure electronic metal-insulator transition at the interface of complex oxides
Authors: Meyers D. , Liu Jian , Freeland J. W. , Middey S. , Kareev M. , Kwon Jihwan , Zuo J. M. , Chuang Yi-De , Kim J. W. , Ryan P. J. , Chakhalian J.
Published: June 2016

In complex materials observed electronic phases and transitions between them often involve coupling between many degrees of freedom whose entanglement convolutes understanding of the instigating mechanism. Metal-insulator transitions are one such problem where coupling to the structural, orbital, charge and magnetic order parameters frequently obscures the underlying physics. Here, we demonstrate a way to unravel this conundrum by heterostructuring a prototypical multi-ordered complex oxide NdNiO3 in ultra thin geometry, which preserves the metal-to-insulator transition and bulk-like magnetic order parameter, but entirely suppresses the symmetry lowering and long-range charge order parameter. These findings illustrate the utility of heterointerfaces as a powerful method for removing competing order parameters to gain greater insight into the nature of the transition, here revealing that the magnetic order generates the transition independently, leading to an exceptionally rare purely electronic metal-insulator transition with no symmetry change.
Multimodal Correlative Preclinical Whole Body Imaging and Segmentation
Authors: Akselrod-Ballin Ayelet , Dafni Hagit , Addadi Yoseph , Biton Inbal , Avni Reut , Brenner Yafit , Neeman Michal
Published: June 2016

Segmentation of anatomical structures and particularly abdominal organs is a fundamental problem for quantitative image analysis in preclinical research. This paper presents a novel approach for whole body segmentation of small animals in a multimodal setting of MR, CT and optical imaging. The algorithm integrates multiple imaging sequences into a machine learning framework, which generates supervoxels by an efficient hierarchical agglomerative strategy and utilizes multiple SVM-kNN classifiers each constrained by a heatmap prior region to compose the segmentation. We demonstrate results showing segmentation of mice images into several structures including the heart, lungs, liver, kidneys, stomach, vena cava, bladder, tumor, and skeleton structures. Experimental validation on a large set of mice and organs, indicated that our system outperforms alternative state of the art approaches. The system proposed can be generalized to various tissues and imaging modalities to produce automatic atlas-free segmentation, thereby enabling a wide range of applications in preclinical studies of small animal imaging.
Suppression of compensating native defect formation during semiconductor processing via excess carriers
Authors: Alberi K. , Scarpulla M. A.
Published: June 2016

In many semiconductors, compensating defects set doping limits, decrease carrier mobility and reduce minority carrier lifetime thus limiting their utility in devices. Native defects are often responsible. Suppressing the concentrations of compensating defects during processing close to thermal equilibrium is difficult because formation enthalpies are lowered as the Fermi level moves towards the majority band edge. Excess carriers, introduced for example by photogeneration, modify the formation enthalpy of semiconductor defects and thus can be harnessed during crystal growth or annealing to suppress defect populations. Herein we develop a rigorous and general model for defect formation in the presence of steady-state excess carrier concentrations by combining the standard quasi-chemical formalism with a detailed-balance description that is applicable for any defect state in the bandgap. Considering the quasi-Fermi levels as chemical potentials, we demonstrate that increasing the minority carrier concentration increases the formation enthalpy for typical compensating centers, thus suppressing their formation. This effect is illustrated for the specific example of GaSb. While our treatment is generalized for excess carrier injection or generation in semiconductors by any means, we provide a set of guidelines for applying the concept in photoassisted physical vapor deposition.