bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emulation of the Saint Venant Equations Enables Rapid and Accurate Predictions of Infiltration and Overland Flow Velocity on Spatially Heterogeneous Surfaces
Authors: Crompton Octavia , Sytsma Anneliese , Thompson Sally 
Published: August 2019

AbstractThe interleaving of impermeable and permeable surfaces along a runoff flow path controls the hillslope hydrograph, the spatial pattern of infiltration, and the distribution of flow velocities in landscapes dominated by overland flow. Predictions of the relationship between the pattern of (im)permeable surfaces and hydrological outcomes tend to fall into two categories: (i) generalized metrics of landscape pattern, often referred to as connectivity metrics, and (ii) direct simulation of specific hillslopes. Unfortunately, the success of using connectivity metrics for prediction is mixed, while direct simulation approaches are computationally expensive and hard to generalize. Here we present a new approach for prediction based on emulation of a coupled Saint Venant equation‐Richards equation model with random forest regression. The emulation model predicts infiltration and peak flow velocities for every location on a hillslope with an arbitrary spatial pattern of impermeable and permeable surfaces but fixed soil, slope, and storm properties. It provides excellent fidelity to the physically based model predictions and is generalizable to novel spatial patterns. The spatial pattern features that explain most of the hydrological variability are not stable across different soils, slopes, and storms, potentially explaining some of the difficulties associated with direct use of spatial metrics for predicting landscape function. Although the current emulator relies on strong assumptions, including smooth topography, binary permeability fields, and only a small collection of soils, slope, and storm scenarios, it offers a promising way forward for applications in dryland and urban settings and in supporting the development of potential connectivity indices.
High proportions of bacteria and archaea across most biomes remain uncultured
Authors: Steen Andrew D , Crits-Christoph Alexander , Carini Paul , DeAngelis Kristen M , Fierer Noah , Lloyd Karen G , Thrash J Cameron 
Published: August 2019

Abstract
A recent paper by Martiny argues that “high proportions” of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer “culturability” because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.
Molecular imaging of oxidative stress using an LED-based photoacoustic imaging system
Authors: Hariri Ali , Zhao Eric , Jeevarathinam Ananthakrishna Soundaram , Lemaster Jeanne , Zhang Jianjian , Jokerst Jesse V. 
Published: August 2019

AbstractLED-based photoacoustic imaging has practical value in that it is affordable and rugged; however, this technology has largely been confined to anatomic imaging with limited applications into functional or molecular imaging. Here, we report molecular imaging reactive oxygen and nitrogen species (RONS) with a near-infrared (NIR) absorbing small molecule (CyBA) and LED-based photoacoustic imaging equipment. CyBA produces increasing photoacoustic signal in response to peroxynitrite (ONOO−) and hydrogen peroxide (H2O2) with photoacoustic signal increases of 3.54 and 4.23-fold at 50 µM of RONS at 700 nm, respectively. CyBA is insensitive to OCl−, ˙NO, NO2−, NO3−, tBuOOH, O2−, C4H9O˙, HNO, and ˙OH, but can detect ONOO− in whole blood and plasma. CyBA was then used to detect endogenous RONS in macrophage RAW 246.7 cells as well as a rodent model; these results were confirmed with fluorescence microscopy. Importantly, CyB suffers photobleaching under a Nd:YAG laser but the signal decrease is <2% with the low-power LED-based photoacoustic system and the same radiant exposure time. To the best of our knowledge, this is the first report to describe molecular imaging with an LED-based photoacoustic scanner. This study not only reveals the sensitive photoacoustic detection of RONS but also highlights the utility of LED-based photoacoustic imaging.
Low-temperature catalyst based Hydrothermal liquefaction of harmful Macroalgal blooms, and aqueous phase nutrient recycling by microalgae
Authors: Kumar Vinod , Kumar Sanjay , Chauhan P. K. , Verma Monu , Bahuguna Vivekanand , Joshi Harish Chandra , Ahmad Waseem , Negi Poonam , Sharma Nishesh , Ramola Bharti , Rautela Indra , Nanda Manisha , Vlaskin Mikhail S. 
Published: August 2019

AbstractThe present study investigates the hydrothermal liquefaction (HTL) of harmful green macroalgal blooms at a temperature of 270 °C with, and without a catalyst with a holding time of 45 min. The effect of different catalysts on the HTL product yield was also studied. Two separation methods were used for recovering the biocrude oil yield from the solid phase. On comparision with other catalyst, Na2CO3 was found to produce higher yiled of bio-oil. The total bio-oil yield was 20.10% with Na2CO3, 18.74% with TiO2, 17.37% with CaO, and 14.6% without a catalyst. The aqueous phase was analyzed for TOC, COD, TN, and TP to determine the nutrient enrichment of water phase for microalgae cultivation. Growth of four microalgae strains viz., Chlorella Minutissima, Chlorella sorokiniana UUIND6, Chlorella singularis UUIND5 and Scenedesmus abundans in the aqueous phase were studied, and compared with a standard growth medium. The results indicate that harmful macroalgal blooms are a suitable feedstock for HTL, and its aqueous phase offers a promising nutrient source for microalgae.
Anthromes displaying evidence of weekly cycles in active fire data cover 70% of the global land surface
Authors: Pereira J. M. C. , Turkman M. A. Amaral , Turkman K. F. , Oom D. 
Published: August 2019

AbstractAcross the globe, human activities have been gaining importance relatively to climate and ecology as the main controls on fire regimes and consequently human activity became an important driver of the frequency, extent and intensity of vegetation burning worldwide. Our objective in the present study is to look for weekly cycles in vegetation fire activity at global scale as evidence of human agency, relying on the original MODIS active fire detections at 1 km spatial resolution (MCD14ML) and using novel statistical methodologies to detect significant periodicities in time series data. We tested the hypotheses that global fire activity displays weekly cycles and that the weekday with the fewest fires is Sunday. We also assessed the effect of land use and land cover on weekly fire cycle significance by testing those hypotheses separately for the Villages, Settlements, Croplands, Rangelands, Seminatural, and Wildlands anthromes. Based on a preliminary data analysis of the daily global active fire counts periodogram, we developed an harmonic regression model for the mean function of daily fire activity and assumed a linear model for the de-seasonalized time series. For inference purposes, we used a Bayesian methodology and constructed a simultaneous 95% credible band for the mean function. The hypothesis of a Sunday weekly minimum was directly investigated by computing the probabilities that the mean functions of every weekday (Monday to Saturday) are inside the credible band corresponding to mean Sunday fire activity. Since these probabilities are small, there is statistical evidence of significantly fewer fires on Sunday than on the other days of the week. Cropland, rangeland, and seminatural anthromes, which cover 70% of the global land area and account for 94% of the active fires analysed, display weekly cycles in fire activity. Due to lower land management intensity and less strict control over fire size and duration, weekly cycles in Rangelands and Seminatural anthromes, which jointly account for 53.46% of all fires, although statistically significant are weaker than those detected in Croplands.
Stability of non-metal dopants to tune the photo-absorption of TiO2 at realistic temperatures and oxygen partial pressures: A hybrid DFT study
Authors: Basera Pooja , Saini Shikha , Arora Ekta , Singh Arunima , Kumar Manish , Bhattacharya Saswata 
Published: August 2019

AbstractTiO2 anatase is considered to play a significant importance in energy and environmental research. However, for developing artificial photosynthesis with TiO2, the major drawback is its large bandgap of 3.2 eV. Several non-metals have been used experimentally for extending the TiO2 photo-absorption to the visible region of the spectrum. It’s therefore of paramount importance to provide theoretical guidance to experiment about the kind of defects that are thermodynamically stable at a realistic condition (e.g. Temperature (T), oxygen partial pressure ($${{\boldsymbol{p}}}_{{{\bf{O}}}_{{\bf{2}}}}$$

p

O

2

), doping). However, disentangling the relative stability of different types of defects (viz. substitution, interstitial, etc.) as a function of charge state and realistic T, $${{\boldsymbol{p}}}_{{{\bf{O}}}_{{\bf{2}}}}$$

p

O

2

is quite challenging. We report here using state-of-the-art first-principles based methodologies, the stability and meta-stability of different non-metal dopants X (X = N, C, S, Se) at various charge states and realistic conditions. The ground state electronic structure is very accurately calculated via density functional theory with hybrid functionals, whereas the finite T and $${{\boldsymbol{p}}}_{{{\bf{O}}}_{{\bf{2}}}}$$

p

O

2

effects are captured by ab initio atomistic thermodynamics under harmonic approximations. On comparing the defect formation energies at a given T and $${{\boldsymbol{p}}}_{{{\bf{O}}}_{{\bf{2}}}}$$

p

O

2

(relevant to the experiment), we have found that Se interstitial defect (with two hole trapped) is energetically most favored in the p-type region, whereas N substitution (with one electron trapped) is the most abundant defect in the n-type region to provide visible region photo-absorption in TiO2. Our finding validates that the most stable defects in X doped TiO2 are not the neutral defects but the charged defects. The extra stability of $${({\bf{S}}{\bf{e}}{\bf{O}})}_{{\bf{O}}}^{+{\bf{2}}}$$

(
S
e
O
)

O

+
2

is carefully analyzed by comparing the individual effect of bond-making/breaking and the charge carrier trapping energies.
Regional mitochondrial DNA and cell-type changes in post-mortem brains of non-diabetic Alzheimer’s disease are not present in diabetic Alzheimer’s disease
Authors: Thubron Elisabeth B. , Rosa Hannah S. , Hodges Angela , Sivaprasad Sobha , Francis Paul T. , Pienaar Ilse S. , Malik Afshan N. 
Published: August 2019

AbstractDiabetes increases the risk of Alzheimer’s disease (AD), and mitochondrial dysfunction is implicated in both diseases, however the impact of both diabetes and AD on brain mitochondria is not known. We measured mitochondrial DNA (mtDNA), an indicator of mitochondrial function, in frontal, parietal, and cerebellar regions of post-mortem human brains (n = 74) from non-cognitively impaired controls (NCI), mild-cognitively impaired (MCI) and AD cases. In a subset of parietal cortices, we measured mRNAs corresponding to cell types and mitochondrial function and semi-automated stereological assessment was performed on immune-staining of parietal cortex sections. mtDNA showed significant regional variation, highest in parietal cortex, and lowest in cerebellum. Irrespective of cognitive status, all brain regions had significantly higher mtDNA in diabetic cases. In the absence of diabetes, AD parietal cortices had decreased mtDNA, reduced MAP2 (neuronal) and increased GFAP (astrocyte) mRNA, relative to NCI. However, in the presence of diabetes, we did not observe these AD-related changes, suggesting that the pathology observed in diabetic AD may be different to that seen in non-diabetic AD. The lack of clear functional changes in mitochondrial parameters in diabetic AD suggest different cellular mechanisms contributing to cognitive impairment in diabetes which remain to be fully understood.
Complex Patterns of Cannabinoid Alkyl Side-Chain Inheritance in Cannabis
Authors: Welling Matthew T. , Liu Lei , Raymond Carolyn A. , Kretzschmar Tobias , Ansari Omid , King Graham J. 
Published: August 2019

AbstractThe cannabinoid alkyl side-chain represents an important pharmacophore, where genetic targeting of alkyl homologs has the potential to provide enhanced forms of Cannabis for biopharmaceutical manufacture. Delta(9)-tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA) synthase genes govern dicyclic (CBDA) and tricyclic (THCA) cannabinoid composition. However, the inheritance of alkyl side-chain length has not been resolved, and few studies have investigated the contributions and interactions between cannabinoid synthesis pathway loci. To examine the inheritance of chemical phenotype (chemotype), THCAS and CBDAS genotypes were scored and alkyl cannabinoid segregation analysed in 210 F2 progeny derived from a cross between two Cannabis chemotypes divergent for alkyl and cyclic cannabinoids. Inheritance patterns of F2 progeny were non-Gaussian and deviated from Mendelian expectations. However, discrete alkyl cannabinoid segregation patterns consistent with digenic as well as epistatic modes of inheritance were observed among F2THCAS and CBDAS genotypes. These results suggest linkage between cannabinoid pathway loci and highlight the need for further detailed characterisation of cannabinoid inheritance to facilitate metabolic engineering of chemically elite germplasm.
Follistatin-based ligand trap ACE-083 induces localized hypertrophy of skeletal muscle with functional improvement in models of neuromuscular disease
Authors: Pearsall R. S. , Davies M. V. , Cannell M. , Li J. , Widrick J. , Mulivor A. W. , Wallner S. , Troy M. E. , Spaits M. , Liharska K. , Sako D. , Castonguay R. , Keates S. , Grinberg A. V. , Suragani R. N. V. S. , Kumar R. 
Published: August 2019

AbstractSkeletal muscle is under inhibitory homeostatic regulation by multiple ligands of the transforming growth factor-β (TGFβ) superfamily. Follistatin is a secreted protein that promotes muscle growth and function by sequestering these ligands extracellularly. In the present study, we evaluated the potential of ACE-083 – a locally acting, follistatin-based fusion protein – as a novel therapeutic agent for focal or asymmetric myopathies. Characterization of ACE-083 in vitro revealed its high affinity for heparin and extracellular matrix while surface plasmon resonance and cell-based assays confirmed that ACE-083 binds and potently neutralizes myostatin, activin A, activin B and growth differentiation factor 11 (GDF11). Intramuscular administration of ACE-083 caused localized, dose-dependent hypertrophy of the injected muscle in wild-type mice and mouse models of Charcot-Marie-Tooth disease (CMT) and Duchenne muscular dystrophy, with no evidence of systemic muscle effects or endocrine perturbation. Importantly, ACE-083 also increased the force of isometric contraction in situ by the injected tibialis anterior muscle in wild-type mice and disease models and increased ankle dorsiflexion torque in CMT mice. Our results demonstrate the potential of ACE-083 as a therapeutic agent for patients with CMT, muscular dystrophy and other disorders with focal or asymmetric muscle atrophy or weakness.
ANAC032 regulates root growth through the MYB30 gene regulatory network
Authors: Maki Hiromasa , Sakaoka Satomi , Itaya Tomotaka , Suzuki Takamasa , Mabuchi Kaho , Amabe Takashi , Suzuki Nobutaka , Higashiyama Tetsuya , Tada Yasuomi , Nakagawa Tsuyoshi , Morikami Atsushi , Tsukagoshi Hironaka 
Published: August 2019

AbstractReactive oxygen species (ROS) play important roles as root growth regulators. We previously reported a comprehensive transcriptomic atlas, which we named ROS-map, that revealed ROS-responsible genes in Arabidopsis root tips. By using ROS-map, we have characterised an early ROS response key transcription factor, MYB30, as a regulator of root cell elongation under ROS signals. However, there are other ROS-responsible transcription factors which have the potential to regulate root growth. In the present study, we characterised the function of another early ROS-responsible transcription factor, ANAC032, that was selected from ROS-map. Overexpression of ANAC032 fused with the transcriptional activation domain, VP16, inhibited root growth, especially decreasing cell elongation. By transcriptome analysis, we revealed that ANAC032 regulated many stress-responsible genes in the roots. Intriguingly, ANAC032 upregulated MYB30 and its target genes. The upregulation of MYB30 target genes was completely abolished in the ANAC032-VP16x2 OX and ANAC032 estradiol-inducible line in myb30-2 mutants. Moreover, root growth inhibition was alleviated in ANAC032-OX in myb30-2 mutants. Overall, we characterised an upstream transcription factor, ANAC032, of the MYB30 transcriptional cascade which is a key regulator for root cell elongation under ROS signalling.
Population-specific long-range linkage disequilibrium in the human genome and its influence on identifying common disease variants
Authors: Park Leeyoung 
Published: August 2019

AbstractDespite the availability of large-scale sequencing data, long-range linkage disequilibrium (LRLD) has not been extensively studied. The theoretical aspects of LRLD estimates were studied to determine the best estimation method for the sequencing data of three different populations of African (AFR), European (EUR), and East-Asian (EAS) descent from the 1000 Genomes Project. Genome-wide LRLDs excluding centromeric regions revealed clear population specificity, presenting substantially more population-specific LRLDs than coincident LRLDs. Clear relationships between the functionalities of the regions in LRLDs denoted long-range interactions in the genome. The proportions of gene regions were increased in LRLD variants, and the coding sequence (CDS)-CDS LRLDs showed obvious functional similarities between genes in LRLDs. Application to theoretical case-control associations confirmed that the LRLDs in genome-wide association studies (GWASs) could contribute to false signals, although the impacts might not be severe in most cases. LRLDs with variants with functional similarity exist in the human genome indicating possible gene-gene interactions, and they differ depending on populations. Based on the current study, LRLDs should be examined in GWASs to identify true signals. More importantly, population specificity in LRLDs should be examined in relevant studies.
Entanglement, holonomic constraints, and the quantization of fundamental interactions
Authors: Giampaolo Salvatore Marco , Macrì Tommaso 
Published: August 2019

AbstractWe provide a proof for the necessity of quantizing fundamental interactions demonstrating that a quantum version is needed for any non trivial conservative interaction whose strength depends on the relative distance between two objects. Our proof is based on a consistency argument that in the presence of a classical field two interacting objects in a separable state could not develop entanglement. This requirement can be cast in the form of a holonomic constraint that cannot be satisfied by generic interparticle potentials. Extending this picture of local holonomic constraints, we design a protocol that allows to measure the terms of a multipole expansion of the interaction of two composite bodies. The results presented in this work can pave the way for a study of fundamental interactions based on the analysis of entanglement properties.
Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vector Culex quinquefasciatus
Authors: Silva Martins Walter Fabricio , Wilding Craig Stephen , Isaacs Alison Taylor , Rippon Emily Joy , Megy Karine , Donnelly Martin James 
Published: August 2019

AbstractCulex quinquefasciatus plays an important role in transmission of vector-borne diseases of public health importance, including lymphatic filariasis (LF), as well as many arboviral diseases. Currently, efforts to tackle C. quinquefasciatus vectored diseases are based on either mass drug administration (MDA) for LF, or insecticide-based interventions. Widespread and intensive insecticide usage has resulted in increased resistance in mosquito vectors, including C. quinquefasciatus. Herein, the transcriptome profile of Ugandan bendiocarb-resistant C. quinquefasciatus was explored to identify candidate genes associated with insecticide resistance. High levels of insecticide resistance were observed for five out of six insecticides tested, with the lowest mortality (0.97%) reported to permethrin, while for DDT, lambdacyhalothrin, bendiocarb and deltamethrin the mortality rate ranged from 1.63–3.29%. Resistance to bendiocarb in exposed mosquitoes was marked, with 2.04% mortality following 1 h exposure and 58.02% after 4 h. Genotyping of the G119S Ace-1 target site mutation detected a highly significant association (p < 0.0001; OR = 25) between resistance and Ace1-119S. However, synergist assays using the P450 inhibitor PBO, or the esterase inhibitor TPP resulted in markedly increased mortality (to ≈80%), suggesting a role of metabolic resistance in the resistance phenotype. Using a novel, custom 60 K whole-transcriptome microarray 16 genes significantly overexpressed in resistant mosquitoes were detected, with the P450 Cyp6z18 showing the highest differential gene expression (>8-fold increase vs unexposed controls). These results provide evidence that bendiocarb resistance in Ugandan C. quinquefasciatus is mediated by both target-site mechanisms and over-expression of detoxification enzymes.
The biomass accumulation and nutrient storage of five plant species in an in-situ phytoremediation experiment in the Ningxia irrigation area
Authors: Chen Chongjuan , Wang Fang , Hong Yu , Liu Ruliang , Luo Liangguo 
Published: August 2019

AbstractPhytoremediation has been widely used and is considered an environmentally friendly and efficient method for mitigating nitrogen (N) and phosphorus (P) loads. However, the technique is rarely employed in the Ningxia irrigation area, which suffers from serious N and P pollution. To investigate ways of protecting the aquatic environment in this region, we conducted in-situ experiments along an agricultural ditch in 2014 and 2015. During the pre-experiment in 2014, five single species floating-bed systems (Zizania latifolia, Oryza sativa, Ipomoea aquatica, Lactuca sativa and Typha latifolia) and one multi-species floating-bed system with three replicates were evaluated over about two months. I. aquatica performed best with respect to biomass accumulation and nutrient storage among all plant systems. Multi-species system was not superior to single species systems: 42% and 37% of the N and P storage in the multi-species system were achieved by I. aquatica. In the formal experiment during 2015, I. aquatica was tested again and performed excellently with respect to biomass production (1.06 kg/m2), N (27.58 g/m2) and P (2.34 g/m2) uptake. Thus, this study demonstrated that I. aquatica could be used to reduce N and P loads under saline and alkaline conditions in the Ningxia irrigation area.