bluuebunny/crossref_metadata_2025 huggingface dataset:
Refining and expanding nonribosomal peptide synthetase function and mechanism
Authors: McErlean Matt , Overbay Jonathan , Van Lanen Steven
Published: January 2019

Nonribosomal peptide synthetases (NRPSs) are involved in the biosynthesis of numerous peptide and peptide-like natural products that have been exploited in medicine, agriculture, and biotechnology, among other fields. As a consequence, there have been considerable efforts aimed at understanding how NRPSs orchestrate the assembly of these natural products. This review highlights several recent examples that continue to expand upon the fundamental knowledge of NRPS mechanism and includes (1) the discovery of new NRPS substrates and the mechanism by which these sometimes structurally complex substrates are made, (2) the characterization of new NRPS activities and domains that function during the process of peptide assembly, and (3) the various catalytic strategies that are utilized to release the NRPS product. These findings continue to strengthen the predictive power for connecting genes to products, thereby facilitating natural product discovery and development in the Genomics Era.
Entrepreneurship capital spillovers at the local level
Authors: Massón-Guerra José Luis , Ortín-Ángel Pedro
Published: January 2019

The paper analyses three underexplored issues in the entrepreneurship capital spillover literature, namely, its local nature, the generators and the receptors of such spillovers. For that purpose, we take advantage of the Ecuadorian census of establishments. Unlike previous evidence, we can estimate the spillovers at the establishment level, compute the entrepreneurship capital at the local level, and compare different permissiveness levels in the application of registration and tax legislation to businesses (i.e., the relative importance of the informal economy). In general, we find entrepreneurship capital spillovers at the local level. The spillover effects are lower when the entrepreneurship capital has been accumulated in informal businesses. By contrast, informal, large and more technologically developed establishments benefit more from these spillover effects. The paper discusses the implications of those findings for the design of public policies for promoting entrepreneurship.
Estimating Multilevel Models on Data Streams
Authors: Ippel L. , Kaptein M. C. , Vermunt J. K.
Published: January 2019

Social scientists are often faced with data that have a nested structure: pupils are nested within schools, employees are nested within companies, or repeated measurements are nested within individuals. Nested data are typically analyzed using multilevel models. However, when data sets are extremely large or when new data continuously augment the data set, estimating multilevel models can be challenging: the current algorithms used to fit multilevel models repeatedly revisit all data points and end up consuming much time and computer memory. This is especially troublesome when predictions are needed in real time and observations keep streaming in. We address this problem by introducing the Streaming Expectation Maximization Approximation (SEMA) algorithm for fitting multilevel models online (or “row-by-row”). In an extensive simulation study, we demonstrate the performance of SEMA compared to traditional methods of fitting multilevel models. Next, SEMA is used to analyze an empirical data stream. The accuracy of SEMA is competitive to current state-of-the-art methods while being orders of magnitude faster.
Erratum to: Decadal glacial lake changes in the Koshi basin, central Himalaya, from 1977 to 2010, derived from Landsat satellite images
Authors: Shrestha Finu , Gao Xiao , Khanal Narendra Raj , Maharjan Sudan Bikash , Shrestha Rajendra Bahadur , Wu Li-zong , Mool Pradeep Kumar , Bajracharya Samjwal Ratna
Published: January 2019

The article Decadal glacial lake changes in the Koshi basin, central Himalaya, from 1977 to 2010, derived from Landsat satellite images, written by Finu SHRESTHA, GAO Xiao, Narendra Raj KHANAL, Sudan Bikash MAHARJAN, Rajendra Bahadur SHRESTHA, WU Li-zong, Pradeep Kumar MOOL and Samjwal Ratna BAJRACHARYA, was originally erroneously published electronically on the publisher’s internet portal (currently SpringerLink) on 04 October 2017 without open access. With the author’s decision to opt for open choice the copyright of the article changed in 01/2019 to © The Author(s) 2019 and the article is forthwith distributed under the terms of the Creative Commons Attribution 4.0 International License
(http://creativecommons.org/licenses/by/4.0/), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The original article has been corrected.
Closing the mass budget of a tidewater glacier: the example of Kronebreen, Svalbard
Authors: DESCHAMPS-BERGER CESAR , NUTH CHRISTOPHER , VAN PELT WARD , BERTHIER ETIENNE , KOHLER JACK , ALTENA BAS
Published: January 2019

In this study, we combine remote sensing, in situ and model-derived datasets from 1966 to 2014 to calculate the mass-balance components of Kronebreen, a fast-flowing tidewater glacier in Svalbard. For the well-surveyed period 2009–2014, we are able to close the glacier mass budget within the prescribed errors. During these 5 years, the glacier geodetic mass balance was −0.69 ± 0.12 m w.e. a−1, while the mass budget method led to a total mass balance of −0.92 ± 0.16 m w.e. a−1, as a consequence of a strong frontal ablation (−0.78 ± 0.11 m w.e. a−1), and a slightly negative climatic mass balance (−0.14 ± 0.11 m w.e. a−1). The trend towards more negative climatic mass balance between 1966–1990 (+0.20 ± 0.05 m w.e. a−1) and 2009–2014 is not reflected in the geodetic mass balance trend. Therefore, we suspect a reduction in ice-discharge in the most recent period. Yet, these multidecadal changes in ice-discharge cannot be measured from the available observations and thus are only estimated with relatively large errors as a residual of the mass continuity equation. Our study presents the multidecadal evolution of the dynamics and mass balance of a tidewater glacier and illustrates the errors introduced by inferring one unmeasured mass-balance component from the others.
Prevalence and predictors of vitamin D deficiency in a nationally representative sample of adults participating in the 2011–2013 Australian Health Survey
Authors: Malacova Eva , Cheang Peihua (Rachel) , Dunlop Eleanor , Sherriff Jill L. , Lucas Robyn M. , Daly Robin M. , Nowson Caryl A. , Black Lucinda J.
Published: January 2019

Vitamin D deficiency is recognised as a public health problem globally, and a high prevalence of deficiency has previously been reported in Australia. This study details the prevalence of vitamin D deficiency in a nationally representative sample of Australian adults aged ≥25 years, using an internationally standardised method to measure serum 25-hydroxyvitamin D (25(OH)D) concentrations and identifies demographic and lifestyle factors associated with vitamin D deficiency. We used data from the 2011–2013 Australian Health Survey (n 5034 with complete information on potential predictors and serum 25(OH)D concentrations). Serum 25(OH)D concentrations were measured by a liquid chromatography-tandem MS that is certified to the reference measurement procedures developed by the National Institute of Standards and Technology, Ghent University and the US Centers for Disease Control and Prevention. Vitamin D deficiency and insufficiency were defined as serum 25(OH)D concentrations <50 nmol/l and 50 to <75 nmol/l, respectively. Overall, 20 % of participants (19 % men; 21 % women) were classified as vitamin D deficient, with a further 43 % classified as insufficient (45 % men; 42 % women). Independent predictors of vitamin D deficiency included being born in a country other than Australia or the main English-speaking countries, residing in southern (higher latitude) states of Australia, being assessed during winter or spring, being obese, smoking (women only), having low physical activity levels and not taking vitamin D or Ca supplements. Given our increasingly indoor lifestyles, there is a need to develop and promote strategies to maintain adequate vitamin D status through safe sun exposure and dietary approaches.
Evaluation of the academic productivity of the top 100 worldwide physicians in the field of otorhinolaryngology and head and neck surgery using the Google Scholar h-index as the bibliometrics ranking system
Authors: Kalcioglu M T , Ileri Y , Ozdamar O I , Yilmaz U , Tekin M
Published: January 2019

Objective

The top 100 physicians of otorhinolaryngology and head and neck surgery worldwide were investigated using the Google Scholar h-index.

Method

Although there are various bibliometrics ranking systems that present the academic quantity and quality of scientists’ published articles, the h-index is the most popular and widely accepted. In this study, Google Scholar was used to search all the keywords involving all the subspecialties of otorhinolaryngology and head and neck surgery, with the aim of identifying as many physicians as possible. Obtaining the Google Scholar h-index and citations is not possible for scientists who do not have Google Scholar accounts. Thus, only those with Google Scholar accounts were included.

Results

The average h-index of all 100 physicians enrolled in the study was 37.83, with a range of 25–81.

Conclusion

The current study details the academic impact of otorhinolaryngology and head and neck surgery physicians worldwide based on the Google Scholar h-index.
Cluster of differentiation 8 T-cell population in the laryngeal mucosa of smokers with laryngeal cancer
Authors: Elwany S , Radi S , Khalil H , Talaat I , Belasy K
Published: January 2019

Objective

To study the cluster of differentiation 8 population in the laryngeal mucosa of patients with laryngeal carcinoma. To our knowledge this is the first paper to address this issue.

Methods

The study group included 40 patients with known laryngeal cancer who were scheduled for laryngectomy. The control groups included 10 smokers and 10 non-smokers who were scheduled for microlaryngeal surgery. Specimens from the three groups were processed for histopathological and histochemical evaluation.

Results

In patients without cancer of the larynx, the number of cluster of differentiation 8 lymphocytes was greater in smokers than non-smokers. The number of cluster of differentiation 8 lymphocytes was greatest in smokers with laryngeal cancer, and the difference between this group and the two control groups was statistically significant.

Conclusion

The study showed that smoking increased the number of cluster of differentiation 8 T-lymphocytes in the laryngeal mucosa. The increase was greatest in patients who had developed laryngeal cancer.
Laser-driven acceleration of heavy ions at ultra-relativistic laser intensity
Authors: Domański J. , Badziak J. , Marchwiany M.
Published: January 2019

This paper presents the results of numerical investigations into the acceleration of heavy ions by a multi-PW laser pulse of ultra-relativistic intensity, to be available with the Extreme Light Infrastructure lasers currently being built in Europe. In the numerical simulations, performed with the use of a multi-dimensional (2D3V) particle-in-cell code, the thorium target with a thickness of 50 or 200 nm was irradiated by a circularly polarized 20 fs laser pulse with an energy of ~150 J and an intensity of 1023 W/cm2. It was found that the detailed run of the ion acceleration process depends on the target thickness, though in both considered cases the radiation pressure acceleration (RPA) stage of ion acceleration is followed by a sheath acceleration stage, with a significant role in the post-RPA stage being played by the ballistic movement of ions. This hybrid acceleration mechanism leads to the production of an ultra-short (sub-picosecond) multi-GeV ion beam with a wide energy spectrum and an extremely high intensity (>1021 W/cm2) and ion fluence (>1017 cm−2). Heavy ion beams of such extreme parameters are hardly achievable in conventional RF-driven ion accelerators, so they could open the avenues to new areas of research in nuclear and high energy density physics, and possibly in other scientific domains.
The structure of priority in the school choice problem
Authors: Duddy Conal
Published: January 2019

In a school choice problem, each school has a priority ordering over the set of students. These orderings depend on criteria such as whether a student lives within walking distance or has a sibling at the school. A priority ordering provides a ranking of students but nothing more. I argue that this information is sufficient when priority is based on merit but not when priority is based on criteria such as walking distance. I propose an extended formulation of the problem wherein a ‘priority matrix’, indicating which criteria are satisfied by each student-school pair, replaces the usual priority orderings.
Strip Intercropping of Rye–Vetch Mixtures: Effects on Weed Growth and Competition in Strip-tilled Sweet Corn
Authors: Lowry Carolyn J. , Brainard Daniel C.
Published: January 2019

Strip-intercropping of functionally diverse cover crop mixtures including cereal rye (Secale cerealeL.) and hairy vetch (Vicia villosaRoth) is one mechanism by which nitrogen (N) banding can be applied to an organic, strip-tilled system to increase crop competitiveness over weeds. We hypothesized that by targeting hairy vetch, a low C:N legume, to the tilled strip directly in row with future crop establishment, and cereal rye, a high C:N grass, to the untilled strip directly between future crop rows, that N would be preferentially available to the crop. We conducted a field study between 2011 to 2013 in southwest Michigan to examine the effects of rye–vetch mixture spatial arrangement (strip intercropping vs. full-width mixture) on (1) soil inorganic N; (2) weed biomass; and (3) sweet corn (Zea maysL.) biomass, yield, and competitiveness against weeds. We found that as the proportion of vetch biomass in the crop row (in-row, IR) increased, we also saw increasing levels of IR soil inorganic N and greater early sweet corn N uptake and growth relative to weeds. However, sweet corn yield and final biomass were more responsive to vetch biomass across the whole plot (WP) and did not respond to rye and vetch segregation into strips. Increasing vetch WP biomass increased sweet corn final biomass across both years, but only increased corn competitiveness against weeds in 1 out of 2 years and decreased sweet corn competitiveness in the other year. Strip-intercropping of cereal rye and hairy vetch has potential to increase soil N availability to the crop, thereby increasing early crop competitiveness, which may lower weed management costs.
Effects of Palmer Amaranth (Amaranthus palmeri) Establishment Time and Distance from the Crop Row on Biological and Phenological Characteristics of the Weed: Implications on Soybean Yield
Authors: Korres Nicholas E. , Norsworthy Jason K. , Mauromoustakos Andy
Published: January 2019

Information about weed biology and weed population dynamics is critical for the development of efficient weed management programs. A field experiment was conducted in Fayetteville, AR, during 2014 and 2015 to examine the effects of Palmer amaranth (Amaranthus palmeriS. Watson) establishment time in relation to soybean [Glycine max(L.) Merr.] emergence and the effects ofA. palmeridistance from the soybean row on the weed’s height, biomass, seed production, and flowering time and on soybean yield. The establishment time factor, in weeks after crop emergence (WAE), was composed of six treatment levels (0, 1, 2, 4, 6, and 8 WAE), whereas the distance from the crop consisted of three treatment levels (0, 24, and 48 cm). Differences inA. palmeribiomass and seed production averaged across distance from the crop were found at 0 and 1 WAE in both years. Establishment time had a significant effect onA. palmeriseed production through greater biomass production and height increases at earlier dates.Amaranthus palmerithat was established with the crop (0 WAE) overtopped soybean at about 7 and 10 WAE in 2014 and 2015, respectively. Distance from the crop affectedA. palmeriheight, biomass, and seed production. The greater the distance from the crop, the higherA. palmeriheight, biomass, and seed production at 0 and 1 WAE compared with other dates (i.e., 2, 4, 6, and 8 WAE).Amaranthus palmeriestablishment time had a significant impact on soybean yield, but distance from the crop did not. The earlierA. palmeriinterfered with soybean (0 and 1 WAE), the greater the crop yield reduction; after that period no significant yield reductions were recorded compared with the rest of the weed establishment times. Knowledge ofA. palmeriresponse, especially at early stages of its life cycle, is important for designing efficient weed management strategies and cropping systems that can enhance crop competitiveness. Control ofA. palmeriwithin the first week after crop emergence or reduced distance between crop and weed are important factors for an effective implementation of weed management measures againstA. palmeriand reduced soybean yield losses due to weed interference.
Bridging the Gap Between Geographical Information Systems and Planetary Virtual Observatory
Authors: Minin M. , Rossi A. P. , Marco Figuera R. , Unnithan V. , Marmo C. , Walter S. H. G. , Demleitner M. , Le Sidaner P. , Cecconi B. , Erard S. , Hare T. M.
Published: January 2019

Virtual Observatory tools are specifically designed for astronomical data, but they can be adapted to work with geospatial data by providing existing Geographical Information System tools with Simple Application Messaging Protocol interface. Open source QGIS package was chosen as a platform for this. The Simple Application Messaging Protocol interface was made with Python plug‐ins. Geospatial data were exposed to Virtual European Solar and Planetary Access via a dedicated German Astronomical Virtual Observatory Data Center Helper Suite server and several tables exposing existing Open Geospatial Consortium—compliant planetary services were published to Virtual European Solar and Planetary Access providing a variety of geospatial data types: vector data and spectral cube rasters, as well as Open Geospatial Consortium Web Map Service of planetary maps.
Drought and Famine in India, 1870–2016
Authors: Mishra Vimal , Tiwari Amar Deep , Aadhar Saran , Shah Reepal , Xiao Mu , Pai D. S. , Lettenmaier Dennis
Published: January 2019

Millions of people died due to famines in India in the nineteenth and twentieth centuries; however, the relationship of historical famines with drought is complicated and not well understood. Using station‐based observations and simulations, we reconstruct soil moisture (agricultural) drought in India for the period 1870–2016. We show that over this century and a half period, India experienced seven major drought periods (1876–1882, 1895–1900, 1908–1924, 1937–1945, 1982–1990, 1997–2004, and 2011–2015) based on severity‐area‐duration analysis of reconstructed soil moisture. Out of six major famines (1873–74, 1876, 1877, 1896–97, 1899, and 1943) that occurred during 1870–2016, five are linked to soil moisture drought, and one (1943) was not. The three most deadly droughts (1877, 1896, and 1899) were linked with the positive phase of El Niño–Southern Oscillation. Five major droughts were not linked with famine, and three of those five nonfamine droughts occurred after Indian independence in 1947.
Saturation Dependence of Non‐Fickian Transport in Porous Media
Authors: Hasan Sharul , Joekar‐Niasar Vahid , Karadimitriou Nikolaos K. , Sahimi Muhammad
Published: January 2019

In two‐phase flow through porous media, the percolating pathways can be hydrodynamically split into the flowing and stagnant regions. The highly variable velocity field in the pore space filled by the carrier fluid leads to significant differences in the transport time scales in the two regions that cannot be explained by the Fickian (Gaussian) advection‐dispersion equation. In contrast with the Darcy‐scale studies, up to now, relatively limited pore‐scale studies have been devoted to the characterization of transport properties in two‐phase flow. In this paper, we report on the results of computer simulation of advection‐dispersion transport in steady state two‐phase flow through porous media using a pore network model, employed as an upscaling tool. The simulation results are upscaled to directly estimate the Darcy‐scale transport coefficients and properties, namely, stagnant saturation, the mass transfer coefficient between the flowing and stagnant regions, and the longitudinal dispersion in the flowing regions. The mobile‐immobile model, one of the most commonly used models for simulating non‐Fickian transport in porous media, is used to estimate the transport properties using the inverse modeling of effluent concentration profiles. The disagreement between the directly estimated parameters and those obtained by the mobile‐immobile‐based inverse modeling implies fundamental shortcomings of the latter for describing transport in two‐phase flow. The simulation results indicate that the relative permeabilities may be used to obtain accurate estimates of the stagnant saturation, which link two‐phase Darcy's law and transport.
Virtual Velocity Approach for Estimating Bed Material Transport in Gravel‐Bed Rivers: Key Factors and Significance
Authors: Brenna A. , Surian N. , Mao L.
Published: January 2019

In large gravel‐bed rivers, bed material transport estimation is challenging since theoretically based formulas often fail to accurately predict sediment fluxes, and it is difficult to carry out field measurements. A viable alternative to direct measurement is provided by the virtual velocity approach representing a hybrid solution to calculate the bed material transport based on a theoretical framework and use of tracers. This work aims to improve the methodology and to assess the role of input factors through a case‐study application carried out in the Parma River (Italy). Two tracer types and scour chains were deployed at four sections. Data on water level, transport processes, particle travel distances, and active layers were collected over 17 months and 6 events. The transport that occurred during two events was calculated applying different configurations taking in account for several input factors (i.e., grain size, water stage, and topography). Applying simple or more complex configurations led to significant differences in transport estimates: In relation to channel morphodynamics, different factors (e.g., variability of water level within the cross section in multithread channels) play a key role on transport processes. Results indicate that it is crucial to collect and process field data developing reach‐specific transport rating curves and to combine different type of tracers for monitoring the clast displacement lengths. Based on the methodological improvements and sensitivity analysis addressed in this study, we developed a decision tree in order to design future applications of the virtual velocity approach for estimating the bed material load in different gravel‐bed river contexts.
Impacts of Subsurface Tile Drainage on Age—Concentration Dynamics of Inorganic Nitrogen in Soil
Authors: Woo Dong K. , Kumar Praveen
Published: January 2019

We explore the impacts of tile drains in agricultural fields on the coupled age and concentration dynamics of nitrate, immobile ammonium, mobile ammonia and ammonium, and nonreactive tracers such as chloride. We implement two mobile interacting pore domains to capture matrix and preferential flow paths in a coupled ecohydrology and biogeochemistry model, Dhara. We apply this model to an agricultural farm that utilizes a corn‐soybean rotation in the Midwestern United States located in the Intensively Managed Landscapes Critical Zone Observatory. In general, we observe both low concentration and age of nitrate in the areas that are classified as topographic depressions even with the presence of tile drains. Also, an increase in the age of mobile ammonia/ammonium is observed after installing tile drains. This is in contrast to the cases for nitrate, immobile ammonium, and nonreactive tracer. These results arise because the depletion of mobile ammonia/ammonium due to tile drainage causes a high mobility flux from immobile ammonium to mobile ammonia/ammonium, which also carries a considerable amount of relatively old age of nitrogen from immobile ammonium to mobile ammonia/ammonium. These results illustrate how storm event scale dynamics impact spatial heterogeneity and temporal variability of the efflux, which helps in disentangling the complexity of nitrogen dynamics in the soil. This understanding can contribute to precision agriculture for nitrogen applications to reduce environmental impacts.
Managing Uncertainties in Climate Engineering
Authors: Kravitz Ben
Published: January 2019

Control theory and climate engineering meet in a new special issue of JGR: Atmospheres.
IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling
Authors: Sheng Xia , Nenseth Hatice Zeynep , Qu Su , Kuzu Omer F. , Frahnow Turid , Simon Lukas , Greene Stephanie , Zeng Qingping , Fazli Ladan , Rennie Paul S. , Mills Ian G. , Danielsen Håvard , Theis Fabian , Patterson John B. , Jin Yang , Saatcioglu Fahri
Published: January 2019

Activation of endoplasmic reticulum (ER) stress/the unfolded protein response (UPR) has been linked to cancer, but the molecular mechanisms are poorly understood and there is a paucity of reagents to translate this for cancer therapy. Here, we report that an IRE1α RNase-specific inhibitor, MKC8866, strongly inhibits prostate cancer (PCa) tumor growth as monotherapy in multiple preclinical models in mice and shows synergistic antitumor effects with current PCa drugs. Interestingly, global transcriptomic analysis reveal that IRE1α-XBP1s pathway activity is required for c-MYC signaling, one of the most highly activated oncogenic pathways in PCa. XBP1s is necessary for optimal c-MYC mRNA and protein expression, establishing, for the first time, a direct link between UPR and oncogene activation. In addition, an XBP1-specific gene expression signature is strongly associated with PCa prognosis. Our data establish IRE1α-XBP1s signaling as a central pathway in PCa and indicate that its targeting may offer novel treatment strategies.
Crystal structure of the plant symporter STP10 illuminates sugar uptake mechanism in monosaccharide transporter superfamily
Authors: Paulsen Peter Aasted , Custódio Tânia F. , Pedersen Bjørn Panyella
Published: January 2019

Plants are dependent on controlled sugar uptake for correct organ development and sugar storage, and apoplastic sugar depletion is a defense strategy against microbial infections like rust and mildew. Uptake of glucose and other monosaccharides is mediated by Sugar Transport Proteins, proton-coupled symporters from the Monosaccharide Transporter (MST) superfamily. We present the 2.4 Å structure of Arabidopsis thaliana high affinity sugar transport protein, STP10, with glucose bound. The structure explains high affinity sugar recognition and suggests a proton donor/acceptor pair that links sugar transport to proton translocation. It contains a Lid domain, conserved in all STPs, that locks the mobile transmembrane domains through a disulfide bridge, and creates a protected environment which allows efficient coupling of the proton gradient to drive sugar uptake. The STP10 structure illuminates fundamental principles of sugar transport in the MST superfamily with implications for both plant antimicrobial defense, organ development and sugar storage.
Clear and transparent nanocrystals for infrared-responsive carrier transfer
Authors: Sakamoto Masanori , Kawawaki Tokuhisa , Kimura Masato , Yoshinaga Taizo , Vequizo Junie Jhon M. , Matsunaga Hironori , Ranasinghe Chandana Sampath Kumara , Yamakata Akira , Matsuzaki Hiroyuki , Furube Akihiro , Teranishi Toshiharu
Published: January 2019

Infrared-light-induced carrier transfer is a key technology for ‘invisible’ optical devices for information communication systems and energy devices. However, clear and colourless photo-induced carrier transfer has not yet been demonstrated in the field of photochemistry, to the best of our knowledge. Here, we resolve this problem by employing short-wavelength-infrared (1400–4000 nm) localized surface plasmon resonance-induced electron injection from indium tin oxide nanocrystals to transparent metal oxides. The time-resolved infrared measurements visualize the dynamics of the carrier in this invisible system. Selective excitation of localized surface plasmon resonances causes hot electron injection with high efficiency (33%) and long-lived charge separation (~ 2–200 μs). We anticipate our study not only provides a breakthrough for plasmonic carrier transfer systems but may also stimulate the invention of state-of-the-art invisible optical devices.
Neuropathological correlates and genetic architecture of microglial activation in elderly human brain
Authors: Felsky Daniel , Roostaei Tina , Nho Kwangsik , Risacher Shannon L. , Bradshaw Elizabeth M. , Petyuk Vlad , Schneider Julie A. , Saykin Andrew , Bennett David A. , De Jager Philip L.
Published: January 2019

Microglia, the resident immune cells of the brain, have important roles in brain health. However, little is known about the regulation and consequences of microglial activation in the aging human brain. Here we report that the proportion of morphologically activated microglia (PAM) in postmortem cortical tissue is strongly associated with β-amyloid, tau-related neuropathology, and the rate of cognitive decline. Effect sizes for PAM measures are substantial, comparable to that of APOE ε4, the strongest genetic risk factor for Alzheimer’s disease, and mediation models support an upstream role for microglial activation in Alzheimer’s disease via accumulation of tau. Further, we identify a common variant (rs2997325) influencing PAM that also affects in vivo microglial activation measured by [11C]-PBR28 PET in an independent cohort. Thus, our analyses begin to uncover pathways regulating resident neuroinflammation and identify overlaps of PAM’s genetic architecture with those of Alzheimer’s disease and several other traits.
Copper amine oxidases catalyze the oxidative deamination and hydrolysis of cyclic imines
Authors: Nagakubo Toshiki , Kumano Takuto , Ohta Takehiro , Hashimoto Yoshiteru , Kobayashi Michihiko
Published: January 2019

Although cyclic imines are present in various bioactive secondary metabolites, their degradative metabolism remains unknown. Here, we report that copper amine oxidases, which are important in metabolism of primary amines, catalyze a cyclic imine cleavage reaction. We isolate a microorganism (Arthrobacter sp. C-4A) which metabolizes a β-carboline alkaloid, harmaline. The harmaline-metabolizing enzyme (HarA) purified from strain C-4A is found to be copper amine oxidase and catalyze a ring-opening reaction of cyclic imine within harmaline, besides oxidative deamination of amines. Growth experiments on strain C-4A and Western blot analysis indicate that the HarA expression is induced by harmaline. We propose a reaction mechanism of the cyclic imine cleavage by HarA containing a post-translationally-synthesized cofactor, topaquinone. Together with the above results, the finding of the same activity of copper amine oxidase from E. coli suggests that, in many living organisms, these enzymes may play crucial roles in metabolism of ubiquitous cyclic imines.
Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer
Authors: Du Qian , Bert Saul A. , Armstrong Nicola J. , Caldon C. Elizabeth , Song Jenny Z. , Nair Shalima S. , Gould Cathryn M. , Luu Phuc-Loi , Peters Timothy , Khoury Amanda , Qu Wenjia , Zotenko Elena , Stirzaker Clare , Clark Susan J.
Published: January 2019

DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.
Membrane reshaping by micrometric curvature sensitive septin filaments
Authors: Beber Alexandre , Taveneau Cyntia , Nania Manuela , Tsai Feng-Ching , Di Cicco Aurelie , Bassereau Patricia , Lévy Daniel , Cabral João T. , Isambert Hervé , Mangenot Stéphanie , Bertin Aurélie
Published: January 2019

Septins are cytoskeletal filaments that assemble at the inner face of the plasma membrane. They are localized at constriction sites and impact membrane remodeling. We report in vitro tools to examine how yeast septins behave on curved and deformable membranes. Septins reshape the membranes of Giant Unilamellar Vesicles with the formation of periodic spikes, while flattening smaller vesicles. We show that membrane deformations are associated to preferential arrangement of septin filaments on specific curvatures. When binding to bilayers supported on custom-designed periodic wavy patterns displaying positive and negative micrometric radii of curvatures, septin filaments remain straight and perpendicular to the curvature of the convex parts, while bending negatively to follow concave geometries. Based on these results, we propose a theoretical model that describes the deformations and micrometric curvature sensitivity observed in vitro. The model captures the reorganizations of septin filaments throughout cytokinesis in vivo, providing mechanistic insights into cell division.
High-throughput single-cell rheology in complex samples by dynamic real-time deformability cytometry
Authors: Fregin Bob , Czerwinski Fabian , Biedenweg Doreen , Girardo Salvatore , Gross Stefan , Aurich Konstanze , Otto Oliver
Published: January 2019

In life sciences, the material properties of suspended cells have attained significance close to that of fluorescent markers but with the advantage of label-free and unbiased sample characterization. Until recently, cell rheological measurements were either limited by acquisition throughput, excessive post processing, or low-throughput real-time analysis. Real-time deformability cytometry expanded the application of mechanical cell assays to fast on-the-fly phenotyping of large sample sizes, but has been restricted to single material parameters as the Young’s modulus. Here, we introduce dynamic real-time deformability cytometry for comprehensive cell rheological measurements at up to 100 cells per second. Utilizing Fourier decomposition, our microfluidic method is able to disentangle cell response to complex hydrodynamic stress distributions and to determine viscoelastic parameters independent of cell shape. We demonstrate the application of our technology for peripheral blood cells in whole blood samples including the discrimination of B- and CD4+ T-lymphocytes by cell rheological properties.
Binder-free graphene oxide doughs
Authors: Yeh Che-Ning , Huang Haiyue , Lim Alane Tarianna O. , Jhang Ren-Huai , Chen Chun-Hu , Huang Jiaxing
Published: January 2019

Graphene oxide (GO) sheets have been used to construct various bulk forms of GO and graphene-based materials through solution-based processing techniques. Here, we report a highly cohesive dough state of GO with tens of weight percent loading in water without binder-like additives. The dough state can be diluted to obtain gels or dispersions, and dried to yield hard solids. It can be kneaded without leaving stains, readily reshaped, connected, and further processed to make bulk GO and graphene materials of arbitrary form factors and tunable microstructures. The doughs can be transformed to dense glassy solids of GO or graphene without long-range stacking order of the sheets, which exhibit isotropic and much enhanced mechanical properties due to hindered sliding between the sheets. GO dough is also found to be a good support material for electrocatalysts as it helps to form compliant interface to access the active particles.
Decrease in radiative forcing by organic aerosol nucleation, climate, and land use change
Authors: Zhu Jialei , Penner Joyce E. , Yu Fangqun , Sillman Sanford , Andreae Meinrat O. , Coe Hugh
Published: January 2019

Organic nucleation is an important source of atmospheric aerosol number concentration, especially in pristine continental regions and during the preindustrial period. Here, we improve on previous simulations that overestimate boundary layer nucleation in the tropics and add changes to climate and land use to evaluate climate forcing. Our model includes both pure organic nucleation and heteromolecular nucleation of sulfuric acid and organics and reproduces the profile of aerosol number concentration measured in the Amazon. Organic nucleation decreases the sum of the total aerosol direct and indirect radiative forcing by 12.5%. The addition of climate and land use change decreases the direct radiative forcing (−0.38 W m−2) by 6.3% and the indirect radiative forcing (−1.68 W m−2) by 3.5% due to the size distribution and number concentration change of secondary organic aerosol and sulfate. Overall, the total radiative forcing associated with anthropogenic aerosols is decreased by 16%.
Sperm-dependent asexual hybrids determine competition among sexual species
Authors: Janko Karel , Eisner Jan , Mikulíček Peter
Published: January 2019

Interspecific competition is a fundamental process affecting community structure and evolution of interacting species. Besides direct competition, this process is also mediated by shared enemies, which can change the outcome of competition dramatically. However, previous studies investigating interactions between competing species and their parasites (parasite-mediated competition) completely overlooked the effect of ‘sperm’ parasites (i.e. sperm-dependent parthenogens or pseudogams) on competition. These organisms originate by interspecific hybridization, produce clonal gametes, but exploit parental species for their own reproduction, being therefore analogous to classical parasites. Here we use the reaction-diffusion model and show that pseudogams alter the outcome of interspecific competition significantly. They may either slow down competitive exclusion of the inferior competitor or even turn the outcome of competition between the species. Asexual organisms may thus have unexpectedly strong impact on community structure, and have more significant evolutionary potential than was previously thought.
Interaction strength promotes robustness against cascading effects in mutualistic networks
Authors: Gaiarsa Marília P. , Guimarães Paulo R.
Published: January 2019

Perturbations, such as fluctuations in abundance, can ripple across species assemblages through ecological interactions. Furthermore, the way in which ecological interactions are organized into a network and the interaction strengths connecting species may be important for cascading effects. Previous work revealed that network structure determines how cascading effects spread across species assemblages. A next step is to understand how interaction strengths influence cascading effects. Here, we assume that perturbations have negative effects, and we evaluate whether interaction strength affects network robustness to cascading effects in mutualistic interactions, and examine the role of network structure in mediating perturbation cascades when interaction strength is incorporated. We combine empirical data on 18 mutualistic networks, two simulations scenarios, and network theory, to investigate how network structure affects perturbation spreading time, a proxy of network robustness to cascading effects. Simulations in which we included interaction strength presented higher mean spreading time, indicating that interaction strength increases network robustness. Richness, modularity, and nestedness had a strong, positive effect, on mean perturbation spreading time regardless of the interaction strengths. We found that network structure and the distribution of interaction strengths affected communities’ robustness to perturbation spreading. Our results contribute to the discussion on the danger that ecosystems face when species, and interactions alike, become extinct.
STAT3-induced upregulation of lncRNA MEG3 regulates the growth of cardiac hypertrophy through miR-361-5p/HDAC9 axis
Authors: Zhang Jingchang , Liang Yi , Huang Xuecheng , Guo Xiaoyan , Liu Yang , Zhong Jiming , Yuan Jielin
Published: January 2019

Cardiac hypertrophy is closely correlated with diverse cardiovascular diseases, augmenting the risk of heart failure and sudden death. Long non-coding RNAs (lncRNAs) have been studied in cardiac hypertrophy for their regulatory function. LncRNA MEG3 has been reported in human cancers. Whereas, it is unknown whether MEG3 regulates the growth of cardiac hypertrophy. Therefore, this study aims to investigate the specific role of MEG3 in the progression of cardiac hypertrophy. Here, we found that MEG3 contributed to the pathogenesis of cardiac hypertrophy. MEG3 expression was remarkably strengthened in the mice heart which undergone the transverse aortic constriction (TAC). Moreover, qRT-PCR analysis revealed that MEG3 was upregulated in the cardiomyocytes which were treated with Ang-II. Silenced MEG3 inhibited the increasing size of hypertrophic cardiomyocytes and reversed other hypertrophic responses. Mechanically, MEG3 could affect cardiac hypertrophy by regulating gene expression. Mechanically, we found that MEG3 could be upregulated by the transcription factor STAT3 and could regulate miR-361-5p and HDAC9 by acting as a ceRNA. Finally, rescue assays were made to do further confirmation. All our findings revealed that STAT3-inducetd upregulation of lncRNA MEG3 controls cardiac hypertrophy by regulating miR-362-5p/HDAC9 axis.
Chinese lantern in Physalis is an advantageous morphological novelty and improves plant fitness
Authors: Li Jing , Song Chunjing , He Chaoying
Published: January 2019

The origin of morphological novelties is an important but neglected issue of evolutionary biology. The fruit of the genus Physalis, a berry, is encapsulated by a novel morphological feature of the post-floral, accrescent calyx that is referred to as a Chinese lantern. The evolutionary developmental genetics of the Chinese lantern have been investigated in the last decade; however, the selective values of the morphological novelty remain elusive. Here, we measured the photosynthetic parameters of the fruiting calyces, monitored microclimatic variation within the Chinese lanterns during fruit development, performed floral-calyx-removal experiments, and recorded the fitness-related traits in Physalis floridana. Ultimately, we show that the green-fruiting calyx of Physalis has photosynthetic capabilities, thus serving as an energy source for fruit development. Moreover, the developing Chinese lantern provides a microclimate that benefits the development and maturation of berry and seed, and it improves plant fitness in terms of fruit/seed weight and number, and fruit maturation under low-temperature environments. Furthermore, the lantern structure facilitates the dispersal of fruits and seeds by water and wind. Our results suggest that the Chinese lantern morphology of Physalis is an evolutionary adaptive trait and improves plant fitness, thus providing new insight into the origin of morphological novelties.
High-temperature operation of a silicon qubit
Authors: Ono Keiji , Mori Takahiro , Moriyama Satoshi
Published: January 2019

This study alleviates the low operating temperature constraint of Si qubits. A qubit is a key element for quantum sensors, memories, and computers. Electron spin in Si is a promising qubit, as it allows both long coherence times and potential compatibility with current silicon technology. Si qubits have been implemented using gate-defined quantum dots or shallow impurities. However, operation of Si qubits has been restricted to milli-Kelvin temperatures, thus limiting the application of the quantum technology. In this study, we addressed a single deep impurity, having strong electron confinement of up to 0.3 eV, using single-electron tunnelling transport. We also achieved qubit operation at 5–10 K through a spin-blockade effect based on the tunnelling transport via two impurities. The deep impurity was implemented by tunnel field-effect transistors (TFETs) instead of conventional FETs. With further improvement in fabrication and controllability, this work presents the possibility of operating silicon spin qubits at elevated temperatures.
The proteome of frozen-thawed pig spermatozoa is dependent on the ejaculate fraction source
Authors: Pérez-Patiño Cristina , Li Junwei , Barranco Isabel , Martínez Emilio A. , Rodriguez-Martínez Heriberto , Roca Jordi , Parrilla Inmaculada
Published: January 2019

The preservation of sperm functional parameters and fertility post-cryopreservation largely varies in the porcine, a species with a fractionated ejaculate. Although intrinsic individual differences have primarily been linked to this variation, differences in protein abundance among frozen-thawed (FT)-spermatozoa are far more relevant. This study, performed in two experiments, looked for proteomic quantitative differences between FT-sperm samples differing in post-thaw viability, motility, apoptosis, membrane lipid peroxidation and nuclear DNA fragmentation. The spermatozoa were either derived from the sperm-rich ejaculate fraction (SRF) or the entire ejaculate (Experiment 1) or from the first 10 mL of the SRF, the remaining SRF and the post-SRF (Experiment 2). Quantitative sperm proteomic differences were analysed using a LC-ESI-MS/MS-based SWATH approach. In Experiment 1, FT-spermatozoa from the SRF showed better preservation parameters than those from the entire ejaculate, with 26Sus scrofaproteins with functional sperm relevance showing relative quantitative differences (FC ≥ 1.5) between sperm sources. In Experiment 2, FT-spermatozoa from the first 10 mL of the SRF and the remaining SRF were qualitatively better than those from the post-SRF, and 187 proteins showed relative quantitative differences among the three ejaculate sources. The results indicate that quantitative proteome differences are linked to sperm cryosurvival.