bluuebunny/crossref_metadata_2025 huggingface dataset:
Snowfall interception in a deciduousNothofagusforest and implications for spatial snowpack distribution
Authors: Huerta Marlene L. , Molotch Noah P. , McPhee James
Published: March 2019

Native Nothofagus forests in the midlatitude region of the Andes Cordillera are notorious biodiversity hot spots, uniquely situated in the Southern Hemisphere such that they develop in snow‐dominated reaches of this mountain range. Spanning a smaller surface area than similar ecosystems, where forests and snow coexist in the Northern Hemisphere, the interaction between vegetation and snow processes in this ecotone has received lesser attention. We present the first systematic study of snow–vegetation interactions in the Nothofagus forests of the Southern Andes, focusing on how the interplay between interception and climate determines patterns of snow water equivalent (SWE) variability. The Valle Hermoso experimental catchment, located in the Nevados de Chillán vicinity, was fitted with eight snow depth sensors that provided continuous measurements at varying elevations, aspect, and forest cover. Also, manual measurements of snow properties were obtained during snow surveys conducted during end of winter and spring seasons for 3 years, between 2015 and 2017. Each year was characterized by distinct climatological conditions, with 2016 representing one of the driest winters on record in this region. Distance to canopy, leaf area index, and total gap area were measured at each observational site. A regression model was built on the basis of statistical analysis of local parameters to model snow interception in this kind of forest. We find that interception implied a 23.2% reduction in snow accumulation in forested sites compared with clearings. The interception in these deciduous trees represents, on average, 23.6% of total annual snowfall, reaching a maximum measured interception value of 13.8‐mm SWE for all snowfall events analysed in this research.
Electromagnetic interference shielding effectiveness and skin depth of poly(vinylidene fluoride)/particulate nano‐carbon filler composites: prediction of electrical conductivity and percolation threshold
Authors: Ram Ranvijai , Khastgir Dipak , Rahaman Mostafizur
Published: March 2019

The addition of various particulate nano‐carbon (PNC) fillers to heat‐resistant poly(vinylidene fluoride) (PVDF) was carried out to prepare conductive composites for use in electromagnetic interference (EMI) shielding application. Three different PNC fillers, namely N472 (Vulcan XC‐72), N550 (Fast Extruding Furnace) and N774 (Semi‐Reinforcing Furnace), were used in various concentrations to prepare composite systems PVDF/N472, PVDF/N550 and PVDF/N774 by solution casting followed by a moulding technique. These PNC fillers have a particle size at the nanometre level, but they have an aggregating tendency; both these characteristics influence the properties of composites to which such fillers are added. The percolation threshold of the PVDF/PNC composites was theoretically determined using the sigmoidal Boltzmann model and classical theory and compared. Theoretical models were also used to predict composition‐dependent electrical conductivity. The electrical conductivity is correlated to that of EMI shielding effectiveness at ambient temperature. © 2019 Society of Chemical Industry
Tuning the Magnetic Exchange Interactions in Organic Biradical Networks
Authors: Baumgarten Martin
Published: March 2019

An overview of organic biradicals directed towards triplon excitations in higher ordered crystalline states is provided. The topic started from the idea to control the intramolecular spin exchange interaction in a sizable but not too large extent, in order to provide also decent intermolecular spin interactions in a crystalline lattice. The predictability of exchange couplings through DFT calculations of optimized geometries turns out to be limited, such that the molecules need to be synthesized and crystallized for further in‐depth characterizations. For crystal structure geometries, most often then a good agreement of calculated intra‐ and intermolecular exchange interactions with those later determined experimentally is found. Finally, it is demonstrated that by choosing well balanced size of both interactions a field‐induced higher ordered magnetic state becomes accessible.
Neuroadaptive containment control of nonlinear multiagent systems with input saturations
Authors: Zhao Lin , Yu Jinpeng , Yu Haisheng , Lin Chong
Published: March 2019

This paper investigates the output containment tracking problem of nonlinear multiagent systems with mismatched uncertain dynamics and input saturations. A neural network–based distributed adaptive command filtered backstepping (CFB) scheme is given, which can guarantee that the containment tracking errors reach to the desired neighborhood of origin and all signals in the closed‐loop system are bounded. Note that error compensation system and virtual control laws established in CFB only use local information, so the given scheme is completely distributed. Moreover, the applied sliding mode differentiator (SMD) can make the outputs of SMD fast approximate the virtual signal and its derivative at each step of backstepping, which can further improve the control quality. Finally, a simulation example is given to show the effectiveness of the proposed scheme.
Optimization in the parallelism extraction algorithm with spanning tree on a multi‐GPU environment
Authors: Wang Guyue , Wada Koichi , Yamagiwa Shinichi
Published: March 2019

This article presents an optimization method of the parallelism extraction algorithm using spanning tree that automatically exploits the parallelism and determines an execution order of multiple kernel programs in a distributed environment. In stream‐based computing, efficient parallel execution requires careful scheduling of the invocation of the kernel programs. By mapping a kernel to a node and an I/O stream to an edge, the entire stream process can be treated as a spanning tree. The spanning tree, which allows feedback and feedforward edges, is effective for expressing dependencies that exist among kernels. In spanning tree, the nodes at the same depth do not have edges between them, and thus can be executed in parallel in the case parent nodes have been already executed. The series of the nodes can be executed in a pipelined manner. Thus, the proposed algorithm can extract both spatial and temporal parallelism. However, if the algorithm is applied for feedbacks as it is, because of waiting for the completion of the loop among the nodes, it causes the waste of time. To solve this problem, the parallel pattern can be optimized in the step of generating the communication pattern to increase the degree of parallelism. In addition, because of the difference in execution time among kernels, the load balancing can be considered for an optimization for the algorithm. To evaluate the effectiveness of the optimized algorithm, a k‐means application was developed and parallelized especially for the feedback processing. The results show that the parallel execution using two nodes of a graphics processing unit (GPU) cluster obtained 1.5 times speedup. With load balancing, the parallel execution using four nodes of the cluster obtained up to 3.5 times speedup in 2D‐FFT and 3.0 times speedup in LU decomposition, compared to the execution on a single GPU. © 2019 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
The peridynamic stress tensors and the non‐local to local passage
Authors: Pelech Petr
Published: March 2019

Motivated by earlier works by S.A. Silling and R.B. Lehoucq, we re‐examine the notion of stress and force flux in peridynamics ‐ a useful connection to measurable quantities and classical view of continuum mechanics. Based on the idea of traction we define two new peridynamic stress tensors and which stand, respectively, for analogues of the Cauchy and 1st Piola‐Kirchhoff stress tensors from classical elasticity. We show that the tensor differs from the earlier defined peridynamic stress tensor ; though their divergence is equal. We address the question of symmetry of the tensor which proves to be symmetric in case of bond‐based peridynamics; as opposed to the inverse Piola transform of  (corresponding to the analogue of Cauchy stress tensor) which fails to be symmetric in general. We also derive a general formula of the force‐flux in peridynamics and compute the limit of  for vanishing non‐locality, denoted by . For the sake of brevity we stick to bond‐based peridynamic in our calculations. We show that this tensor surprisingly coincides with the collapsed tensor , the limit of the original tensor . At the end, using this flux‐formula, we suggest an explanation why the collapsed tensor (and hence ) can be indeed identified with the 1st Piola‐Kirchhoff stress tensor. Throughout the whole paper we suppose that the deformation is sufficiently regular.
Intraoperative Flash Visual Evoked Potential Recording and Relationship to Visual Outcome
Authors: Houlden David A. , Turgeon Chantal A. , Amyot Nathaniel S. , Edem Idara , Sinclair John , Agbi Charles , Polis Thomas , Alkherayf Fahad
Published: March 2019

Objective: To determine the relationship between intraoperative flash visual evoked potential (FVEP) monitoring and visual function. Methods: Intraoperative FVEPs were recorded from electrodes placed in the scalp overlying the visual cortex (Oz) after flashing red light stimulation delivered by Cadwell LED stimulating goggles in 89 patients. Restrictive filtering (typically 10–100 Hz), optimal reject window settings, mastoid reference site, total intravenous anesthetic (TIVA), and stable retinal stimulation (ensured by concomitant electroretinogram [ERG] recording) were used to enhance FVEP reproducibility. Results: The relationship between FVEP amplitude change and visual outcome was determined from 179 eyes. One eye had a permanent intraoperative FVEP loss despite stable ERG, and this eye had new, severe postoperative visual dysfunction. Seven eyes had transient significant FVEP change (>50% amplitude decrease that recovered by the end of surgery), but only one of those had a decrease in postoperative visual acuity. FVEP changes in all eight eyes (one permanent FVEP loss plus seven transient FVEP changes) were related to surgical manipulation. In each case the surgeon was promptly informed of the FVEP deterioration and took remedial action. The other eyes did not have FVEP changes, and none of those eyes had new postoperative visual deficits. Conclusions: Our FVEP findings relate to visual outcome with a sensitivity and specificity of 1.0. New methods for rapidly acquiring reproducible FVEP waveforms allowed for timely reporting of significant FVEP change resulting in prompt surgical action. This may have accounted for the low postoperative visual deficit rate (1%) in this series.
Working around the Law: Navigating Legal Barriers to Employment during Reentry
Authors: Augustine Dallas
Published: March 2019

Employment has been cited as one of the most effective protections against recidivism for formerly incarcerated people; however, job seekers with criminal records face barriers to employment after prison. They find themselves in a legal double bind where they are simultaneously compelled to obey the law (by finding “legit” work) but also legally barred from doing so. To navigate this conflictual legal positioning, job seekers with felony records develop strategies of working around the law to find employment. Through thirty qualitative interviews with people with felony records, I examine this alternative form of legal consciousness and detail the ways in which individuals navigate the legal barriers to acquiring “good” work. Ultimately, job seekers’ often extralegal strategies of law abidance blur the line between compliance with and defiance of the law.
The Dark Side of the Moon: Nationalism, Human Rights, and the Erased Residents of Slovenia
Authors: Gornik Barbara
Published: March 2019

In 1992, after the dissolution of Socialist Federal Republic of Yugoslavia, the Slovenian government unlawfully erased 25,671 individuals—ethnically mainly Serbs, Croats, Bosnians, Macedonians, Montenegrins, and Roma—from the Register of Permanent Residents of Slovenia. The aim of this article is to analyze the logic of the governmental rationalities that served as a basis for the politics of the erasure. The article begins by refuting claims that the erasure was a tactic for achieving ethnocultural homogeneity and continues by explaining the mindset involved in this particular practice of government, resting upon Foucault’s notions ofraison d’état, governmentality, and sovereign power. Highlighting the prominence of the individual’s political opinion and loyalty to the newly established state, the article discusses the principles of nationalism, which reinforce the very common-sense exclusionary politics related to political loyalty implied in citizenship and ethnic identity. Finally, the article deliberates on the effects of the contemporary diagram of power of the nation-state, which legitimizes the exclusion of individuals from the national polity and thus immobilizes universal respect of human rights.
Unusually variable paleocommunity composition in the oldest metazoan fossil assemblages
Authors: Finnegan Seth , Gehling James G. , Droser Mary L.
Published: March 2019

Recent excavations of Ediacaran assemblages have revealed striking bed-to-bed variation in diversity–abundance structure, offering potential insight into the ecology and taphonomy of these poorly understood early Metazoan ecosystems. Here we compare faunal variability in Ediacaran assemblages to that of younger benthic assemblages, both fossil and modern. We decompose the diversity of local assemblages into within-collection (α) and among-collection (β) components and show that β diversity in Ediacaran assemblages is unusually high relative to younger assemblages. Average between-bed ecological dissimilarities in the Phanerozoic fossil record are comparable to within-habitat dissimilarities typically observed over meter to kilometer scales in modern benthic marine habitats, but dissimilarities in Ediacaran assemblages are comparable to those typically observed over 10–100 km scales in modern habitats. We suggest that the unusually variable diversity–abundance structure of Ediacaran assemblages is due both to their preservation as near snapshots of benthic communities and to original ecological differences, in particular the paucity of motile taxa and the near lack of predation and infaunalization.
Carolina Redroot (Lachnanthes caroliniana) in Cranberry: Assessment of Shoot and Rhizome Control with POST Herbicides
Authors: Besançon Thierry E.
Published: March 2019

Carolina redroot is a common weed of New Jersey cranberry beds that competes with crops for nutritional resources but also serves as a food source for waterfowl. Greenhouse studies were conducted in 2017 in Chatsworth, NJ, to determine control of Carolina redroot aboveground vegetation and rhizome production with 10 herbicide active ingredients. Herbicides were applied as a single application on 10- to 15-cm-tall plants. Diquat at 560 g ai ha−1and mesotrione at 280 or 560 g ai ha−1controlled more than 90% of emerged shoots at 63 d after treatment (DAT). Aboveground vegetation control at 63 DAT reached 87% with 2,4-D and flumioxazin but was limited with glyphosate, not exceeding 40%. Mesotrione at 560 g ai ha−1provided 98% control of roots and rhizomes (root/rhizome) at 63 DAT, a 10% increase compared with 280 g ai ha−1; and 2,4-D (90%), glyphosate (87%), diquat (86%), and flumioxazin (85%) also showed excellent root/rhizome control. The greatest reduction of plant biomass compared with the nontreated check (UNT) was noted with 2,4-D, mesotrione at 280 g ai ha−1and 560 g ai ha−1, and diquat, with decreases from 73% to 80% for shoots and from 82% to 88% for roots/rhizomes. Glyphosate had less impact on shoot biomass reduction (−56%) but similar effect on root/rhizome dry weight (−79%) compared with 2,4-D, mesotrione, and diquat. Flumioxazin and fomesafen significantly reduced root/rhizome biomass by 78% and 72%, respectively. Concurrently, 2,4-D, flumioxazin, fomesafen, and diquat reduced the number of secondary shoots 70% to 90% compared with the UNT, whereas glyphosate and mesotrione completely inhibited emergence of new shoots. These data suggest that mesotrione applied POST provides excellent control of Carolina redroot. Future research should evaluate field applications of mesotrione in early summer when Carolina redroot regrowth occurs following the dissipation of PRE herbicide activity.
Long‐Term Consistent Monthly Temperature and Precipitation Grid Data Sets for Switzerland Over the Past 150 Years
Authors: Isotta Francesco A. , Begert Michael , Frei Christoph
Published: March 2019

For some applications, long‐term coverage and climate consistency are important requirements in gridded climate data sets. This is often challenged by the inhomogeneity of measurements and by the variation of station networks over time. We describe the development of new monthly grid data sets of temperature and precipitation for Switzerland that range back as far as 1864 and satisfy high standards in long‐term consistency. To this end, data are incorporated from stations only with complete and homogenized series available. To compensate for the limited spatial coverage, our analysis integrates statistical information from high‐resolution grid data sets based on a dense network but over a limited period. For Switzerland, we demonstrate that the statistical reconstruction recovers mesoscale features not resolved by the stations alone. The method is fairly robust against representativity biases during calibration. The resulting trend maps are more plausible than those from common interpolation with more extensive but variable station networks. Typical errors in the analyses are 0.2 °C for monthly temperature and 10% for precipitation, but they can be larger in regions with low station density. In 75% of all months, the reconstructions explain more than 90% of the spatial variance for temperature and more than 60% for precipitation. From the new data sets, we infer a warming trend of around 1.3 °C per century in the period 1864–2017, increasing to more than 0.35 °C per decade for 1961–2017. Precipitation trends are not statistically significant, except in winter, when an increase of 1–3% per decade is found in the north and west of the country.
Changing Name for Earth’s Changing Poles
Authors: Kornprobst Jacques , L�nat Jean-Fran�ois
Published: March 2019

The name of one geomagnetic pole reversal, the Laschamps excursion, somehow lost its s as it wandered through the scientific literature. It’s time to set the record straight.
Indirect optical trapping using light driven micro-rotors for reconfigurable hydrodynamic manipulation
Authors: Būtaitė Unė G. , Gibson Graham M. , Ho Ying-Lung D. , Taverne Mike , Taylor Jonathan M. , Phillips David B.
Published: March 2019

Optical tweezers are a highly versatile tool for exploration of the mesoscopic world, permitting non-contact manipulation of nanoscale objects. However, direct illumination with intense lasers restricts their use with live biological specimens, and limits the types of materials that can be trapped. Here we demonstrate an indirect optical trapping platform which circumvents these limitations by using hydrodynamic forces to exert nanoscale-precision control over aqueous particles, without directly illuminating them. Our concept is based on optically actuated micro-robotics: closed-loop control enables highly localised flow-fields to be sculpted by precisely piloting the motion of optically-trapped micro-rotors. We demonstrate 2D trapping of absorbing particles which cannot be directly optically trapped, stabilise the position and orientation of yeast cells, and demonstrate independent control over multiple objects simultaneously. Our work expands the capabilities of optical tweezers platforms, and represents a new paradigm for manipulation of aqueous mesoscopic systems.
A reference-grade wild soybean genome
Authors: Xie Min , Chung Claire Yik-Lok , Li Man-Wah , Wong Fuk-Ling , Wang Xin , Liu Ailin , Wang Zhili , Leung Alden King-Yung , Wong Tin-Hang , Tong Suk-Wah , Xiao Zhixia , Fan Kejing , Ng Ming-Sin , Qi Xinpeng , Yang Linfeng , Deng Tianquan , He Lijuan , Chen Lu , Fu Aisi , Ding Qiong , He Junxian , Chung Gyuhwa , Isobe Sachiko , Tanabata Takanari , Valliyodan Babu , Nguyen Henry T. , Cannon Steven B. , Foyer Christine H. , Chan Ting-Fung , Lam Hon-Ming
Published: March 2019

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.
Dissecting features of epigenetic variants underlying cardiometabolic risk using full-resolution epigenome profiling in regulatory elements
Authors: Allum Fiona , Hedman Åsa K. , Shao Xiaojian , Cheung Warren A. , Vijay Jinchu , Guénard Frédéric , Kwan Tony , Simon Marie-Michelle , Ge Bing , Moura Cristiano , Boulier Elodie , Rönnblom Lars , Bernatsky Sasha , Lathrop Mark , McCarthy Mark I. , Deloukas Panos , Tchernof André , Pastinen Tomi , Vohl Marie-Claude , Grundberg Elin
Published: March 2019

Sparse profiling of CpG methylation in blood by microarrays has identified epigenetic links to common diseases. Here we apply methylC-capture sequencing (MCC-Seq) in a clinical population of ~200 adipose tissue and matched blood samples (Ntotal~400), providing high-resolution methylation profiling (>1.3 M CpGs) at regulatory elements. We link methylation to cardiometabolic risk through associations to circulating plasma lipid levels and identify lipid-associated CpGs with unique localization patterns in regulatory elements. We show distinct features of tissue-specific versus tissue-independent lipid-linked regulatory regions by contrasting with parallel assessments in ~800 independent adipose tissue and blood samples from the general population. We follow-up on adipose-specific regulatory regions under (1) genetic and (2) epigenetic (environmental) regulation via integrational studies. Overall, the comprehensive sequencing of regulatory element methylomes reveals a rich landscape of functional variants linked genetically as well as epigenetically to plasma lipid traits.
Memory and relatedness of transcriptional activity in mammalian cell lineages
Authors: Phillips Nicholas E. , Mandic Aleksandra , Omidi Saeed , Naef Felix , Suter David M.
Published: March 2019

Phenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. How transcriptional activity propagates in cell lineages, and how this varies across genes is poorly understood. Here we combine live-cell imaging of short-lived transcriptional reporters in mouse embryonic stem cells with mathematical modelling to quantify the propagation of transcriptional activity over time and across cell generations in phenotypically homogenous cells. In sister cells we find mean transcriptional activity to be strongly correlated and transcriptional dynamics tend to be synchronous; both features control how quickly transcriptional levels in sister cells diverge in a gene-specific manner. Moreover, mean transcriptional activity is transmitted from mother to daughter cells, leading to multi-generational transcriptional memory and causing inter-family heterogeneity in gene expression.
Peptidomic and glycomic profiling of commercial dairy products: identification, quantification and potential bioactivities
Authors: Bhattacharya Mrittika , Salcedo Jaime , Robinson Randall C. , Henrick Bethany Michele , Barile Daniela
Published: March 2019

Peptidomics and glycomics are recently established disciplines enabling researchers to characterize functional characteristics of foods at a molecular level. Milk-derived bioactive peptides and oligosaccharides have garnered both scientific and commercial interest because they possess unique functional properties, such as anti-hypertensive, immunomodulatory and prebiotic activities; therefore, the objective of this work was to employ peptidomic and glycomic tools to identify and measure relative and absolute quantities of peptides and oligosaccharides in widely consumed dairy products. Specifically, we identified up to 2117 unique peptides in 10 commercial dairy products, which together represent the most comprehensive peptidomic profiling of dairy milk in the literature to date. The quantity of peptides, measured by ion-exchange chromatography, varied between 60 and 130 mg/L among the same set of dairy products, which the majority originated from caseins, and the remaining from whey proteins. A recently published bioactive peptide database was used to identify 66 unique bioactive peptides in the dataset. In addition, 24 unique oligosaccharide compositions were identified in all the samples by nano LC Chip QTOF. Neutral oligosaccharides were the most abundant class in all samples (66–91.3%), followed by acidic (8.6–33.7%), and fucosylated oligosaccharides (0–4.6%). Variation of total oligosaccharide concentration ranged from a high of 65.78 to a low of 24.82 mg/L. Importantly, characterizing bioactive peptides and oligosaccharides in a wider number of dairy products may lead to innovations that go beyond the traditional vision of dairy components used for nutritional purposes but that will rather focus on improving human health.
Elevated pre-activation basal level of nuclear NF-κB in native macrophages accelerates LPS-induced translocation of cytosolic NF-κB into the cell nucleus
Authors: Bagaev Alexander V. , Garaeva Anastasiya Y. , Lebedeva Ekaterina S. , Pichugin Alexey V. , Ataullakhanov Ravshan I. , Ataullakhanov Fazly I.
Published: March 2019

Signaling via Toll-like receptor 4 (TLR4) in macrophages constitutes an essential part of the innate immune response to bacterial infections. Detailed and quantified descriptions of TLR4 signal transduction would help to understand and exploit the first-line response of innate immune defense. To date, most mathematical modelling studies were performed on transformed cell lines. However, properties of primary macrophages differ significantly. We therefore studied TLR4-dependent activation of NF-κB transcription factor in bone marrow-derived and peritoneal primary macrophages. We demonstrate that the kinetics of NF-κB phosphorylation and nuclear translocation induced by a wide range of bacterial lipopolysaccharide (LPS) concentrations in primary macrophages is much faster than previously reported for macrophage cell lines. We used a comprehensive combination of experiments and mathematical modeling to understand the mechanisms of this rapid response. We found that elevated basal NF-κB in the nuclei of primary macrophages is a mechanism increasing native macrophage sensitivity and response speed to the infection. Such pre-activated state of macrophages accelerates the NF-κB translocation kinetics in response to low agonist concentrations. These findings enabled us to refine and construct a new model combining both NF-κB phosphorylation and translocation processes and predict the existence of a negative feedback loop inactivating phosphorylated NF-κB.
Association Between Radiomics Signature and Disease-Free Survival in Conventional Papillary Thyroid Carcinoma
Authors: Park Vivian Y. , Han Kyunghwa , Lee Eunjung , Kim Eun-Kyung , Moon Hee Jung , Yoon Jung Hyun , Kwak Jin Young
Published: March 2019

Patients with papillary thyroid carcinoma (PTC) would benefit from risk stratification tools that can aid in planning personalized treatment and follow-up. The aim of this study was to develop a conventional ultrasound (US)-based radiomics signature to estimate disease-free survival (DFS) in patients with conventional PTC. Imaging features were extracted from the pretreatment US images of 768 patients with conventional PTC who were treated between January 2004 and February 2006. The median follow-up period was 117.3 months, with 85 (11.1%) events. A radiomics signature (Rad-score) was generated by using the least absolute shrinkage and selection operator (LASSO) method in Cox regression. The Rad-score was significantly associated with DFS (hazard ratio [HR], 3.087; P < 0.001), independent of clinicopathologic risk factors. A radiomics model which incorporated the Rad-score demonstrated better performance in the estimation of DFS (C-index: 0.777; 95% confidence interval [CI]: 0.735, 0.829) than the clinicopathologic model (C-index: 0.721; 95% CI: 0.675, 0.780). In conclusion, radiomics features from pretreatment US may be potential imaging biomarkers for risk stratification in patients with conventional PTC.
Deep-UV to Mid-IR Supercontinuum Generation driven by Mid-IR Ultrashort Pulses in a Gas-filled Hollow-core Fiber
Authors: Adamu Abubakar I. , Habib Md. Selim , Petersen Christian R. , Lopez J. Enrique Antonio , Zhou Binbin , Schülzgen Axel , Bache Morten , Amezcua-Correa Rodrigo , Bang Ole , Markos Christos
Published: March 2019

Supercontinuum (SC) generation based on ultrashort pulse compression constitutes one of the most promising technologies towards ultra-wide bandwidth, high-brightness, and spatially coherent light sources for applications such as spectroscopy and microscopy. Here, multi-octave SC generation in a gas-filled hollow-core antiresonant fiber (HC-ARF) is reported spanning from 200 nm in the deep ultraviolet (DUV) to 4000 nm in the mid-infrared (mid-IR) having an output energy of 5 μJ. This was obtained by pumping at the center wavelength of the first anti-resonant transmission window (2460 nm) with ~100 fs pulses and an injected pulse energy of ~8 μJ. The mechanism behind the extreme spectral broadening relies upon intense soliton-plasma nonlinear dynamics which leads to efficient soliton self-compression and phase-matched dispersive wave (DW) emission in the DUV region. The strongest DW is observed at 275 nm which corresponds to the calculated phase-matching wavelength of the pump. Furthermore, the effect of changing the pump pulse energy and gas pressure on the nonlinear dynamics and their direct impact on SC generation was investigated. This work represents another step towards gas-filled fiber-based coherent sources, which is set to have a major impact on applications spanning from DUV to mid-IR.
Ubiquity of anomalous transport in porous media: Numerical evidence, continuous time random walk modelling, and hydrodynamic interpretation
Authors: Yang Xiao-Rong , Wang Yan
Published: March 2019

Anomalous transport in porous media is commonly believed to be induced by the highly complex pore space geometry. However, this phenomenon is also observed in porous media with rather simple pore structure. In order to answer how ubiquitous can anomalous transport be in porous media, we in this work systematically investigate the solute transport process in a simple porous medium model with minimal structural randomness. The porosities we consider range widely from 0.30 up to 0.85, and we find by lattice Boltzmann simulations that the solute transport process can be anomalous in all cases at high Péclet numbers. We use the continuous time random walk theory to quantitatively explain the observed scaling relations of the process. A plausible hydrodynamic origin of anomalous transport in simple porous media is proposed as a complement to its widely accepted geometric origin in complex porous media. Our results, together with previous findings, provide evidence that anomalous transport is indeed ubiquitous in porous media. Consequently, attentions should be paid when modelling solute transport by the classical advection-diffusion equation, which could lead to systematic error.
Chromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures
Authors: Oliveira Samuel M. D. , Goncalves Nadia S. M. , Kandavalli Vinodh K. , Martins Leonardo , Neeli-Venkata Ramakanth , Reyelt Jan , Fonseca Jose M. , Lloyd-Price Jason , Kranz Harald , Ribeiro Andre S.
Published: March 2019

Temperature shifts trigger genome-wide changes in Escherichia coli’s gene expression. We studied if chromosome integration impacts on a gene’s sensitivity to these shifts, by comparing the single-RNA production kinetics of a PLacO3O1 promoter, when chromosomally-integrated and when single-copy plasmid-borne. At suboptimal temperatures their induction range, fold change, and response to decreasing temperatures are similar. At critically low temperatures, the chromosome-integrated promoter becomes weaker and noisier. Dissection of its initiation kinetics reveals longer lasting states preceding open complex formation, suggesting enhanced supercoiling buildup. Measurements with Gyrase and Topoisomerase I inhibitors suggest hindrance to escape supercoiling buildup at low temperatures. Consistently, similar phenomena occur in energy-depleted cells by DNP at 30 °C. Transient, critically-low temperatures have no long-term consequences, as raising temperature quickly restores transcription rates. We conclude that the chromosomally-integrated PLacO3O1 has higher sensitivity to low temperatures, due to longer-lasting super-coiled states. A lesser active, chromosome-integrated native lac is shown to be insensitive to Gyrase overexpression, even at critically low temperatures, indicating that the rate of escaping positive supercoiling buildup is temperature and transcription rate dependent. A genome-wide analysis supports this, since cold-shock genes exhibit atypical supercoiling-sensitivities. This phenomenon might partially explain the temperature-sensitivity of some transcriptional programs of E. coli.
Wild sea otter mussel pounding leaves archaeological traces
Authors: Haslam Michael , Fujii Jessica , Espinosa Sarah , Mayer Karl , Ralls Katherine , Tinker M. Tim , Uomini Natalie
Published: March 2019

Wild sea otters (Enhydra lutris) are the only marine mammals that habitually use stones while foraging, using them to break open hard-shelled foods like marine snails and bivalves. However, the physical effects of this behavior on local environments are unknown. We show that sea otters pounding mussels on tidally emergent rocks leave distinct material traces, which can be recognized using methods from archaeology. We observed sea otters pounding mussels at the Bennett Slough Culverts site, California, USA, over a l0-year period. Sea otters repeatedly used the same rocks as anvils, which resulted in distinctive wear patterns on the rocks and accumulations of broken mussel shells, all fractured in a characteristic way, below them. Our results raise the potential for discovery of similar sea otter pounding sites in areas that no longer have resident sea otter populations.
Contemporary limnology of the rapidly changing glacierized watershed of the world’s largest High Arctic lake
Authors: St. Pierre K. A. , St. Louis V. L. , Lehnherr I. , Schiff S. L. , Muir D. C. G. , Poulain A. J. , Smol J. P. , Talbot C. , Ma M. , Findlay D. L. , Findlay W. J. , Arnott S. E. , Gardner Alex S.
Published: March 2019

Glacial runoff is predicted to increase in many parts of the Arctic with climate change, yet little is known about the biogeochemical impacts of meltwaters on downstream freshwater ecosystems. Here we document the contemporary limnology of the rapidly changing glacierized watershed of the world’s largest High Arctic lake (Lake Hazen), where warming since 2007 has increased delivery of glacial meltwaters to the lake by up to 10-times. Annually, glacial meltwaters accounted for 62–98% of dissolved nutrient inputs to the lake, depending on the chemical species and year. Lake Hazen was a strong sink for NO3−-NO2−, NH4+ and DOC, but a source of DIC to its outflow the Ruggles River. Most nutrients entering Lake Hazen were, however, particle-bound and directly transported well below the photic zone via dense turbidity currents, thus reinforcing ultraoligotrophy in the lake rather than overcoming it. For the first time, we apply the land-to-ocean aquatic continuum framework in a large glacierized Arctic watershed, and provide a detailed and holistic description of the physical, chemical and biological limnology of the rapidly changing Lake Hazen watershed. Our findings highlight the sensitivity of freshwater ecosystems to the changing cryosphere, with implications for future water quality and productivity at high latitudes.
Atmospheric ammonia (NH3) emanations from Lake Natron’s saline mudflats
Authors: Clarisse L. , Van Damme M. , Gardner W. , Coheur P.-F. , Clerbaux C. , Whitburn S. , Hadji-Lazaro J. , Hurtmans D.
Published: March 2019

In a recent global analysis of satellite-derived atmospheric NH3 data, a hotspot was observed in the vicinity of Lake Natron, Tanzania. The lake is in the centre of an endorheic (limited drainage) basin and has shallow, saline-alkaline waters. Its remote location and the absence of nearby large anthropogenic sources suggest that the observed NH3 is mainly of natural origin. Here we explore 10 years of IASI NH3 satellite data and other publicly available datasets over the area to characterize the natural NH3 emissions in this unique ecosystem. Temporal analysis reveals that the emissions are episodic and linked with the lake’s surface area. The largest NH3 column loadings generally occur at the end of the dry season in September–November over Lake Natron’s largest mudflat, that is exposed with receding water levels. The timing is different from the agricultural dominated NH3 emissions in the wider Natron area, which peak early in the year, after the first wet season. The likely source of NH3 at Lake Natron is decomposition of organic material, either from rivers and springs or produced in the lake (plankton, bird excreta). High temperatures and alkalinity are known to promote NH3 losses from soda lakes. We formulate six processes that may explain why the largest losses are observed specifically over concentrated brines and/or exposed sediments. As a by-product, we also show that hyperspectral infrared sounders such as IASI are capable of mapping different types of evaporative minerals such as trona and thermonatrite.
Intrinsic activation of cell growth and differentiation in ex vivo cultured human hair follicles by a transient endogenous production of ROS
Authors: Calvo-Sánchez María I. , Fernández-Martos Sandra , Montoya Juan José , Espada Jesús
Published: March 2019

The emerging variety of signalling roles for ROS in eukaryotic cells and tissues is currently a matter of intense research. Here we make use of ex vivo cultured single human hair follicles as an experimental model to demonstrate that a transient production of non-lethal endogenous ROS levels in these mini-organs promotes efficiently the entry into the growth phase (anagen). The stimulatory process implicates the specific activation of the hair follicle stem cell niche, encompassing the induction of stem cell differentiation markers (Ck15), overall cell proliferation and sustained growth of the tissue associated with expression of gen targets (Ccnd1) concomitant with the inhibition of Wnt signaling antagonists and repressors (Dkk1, Gsk3β) of Wnt signaling. As a whole, this observation indicates that, once activated, ROS signalling is an intrinsic mechanism regulating the hair follicle stem cell niche independently of any external signal.
Functional divergence of thyrotropin beta-subunit paralogs gives new insights into salmon smoltification metamorphosis
Authors: Fleming Mitchell S. , Maugars Gersende , Lafont Anne-Gaëlle , Rancon Jocelyn , Fontaine Romain , Nourizadeh-Lillabadi Rasoul , Weltzien Finn-Arne , Yebra-Pimentel Elena Santidrian , Dirks Ron , McCormick Stephen D. , Rousseau Karine , Martin Patrick , Dufour Sylvie
Published: March 2019

Smoltification is a metamorphic event in salmon life history, which initiates downstream migration and pre-adapts juvenile salmon for seawater entry. While a number of reports concern thyroid hormones and smoltification, few and inconclusive studies have addressed the potential role of thyrotropin (TSH). TSH is composed of a α-subunit common to gonadotropins, and a β-subunit conferring hormone specificity. We report the presence and functional divergence of duplicated TSH β-subunit paralogs (tshβa and tshβb) in Atlantic salmon. Phylogeny and synteny analyses allowed us to infer that they originated from teleost-specific whole genome duplication. Expression profiles of both paralogs in the pituitary were measured by qPCR throughout smoltification in Atlantic salmon from the endangered Loire-Allier population raised in a conservation hatchery. This revealed a striking peak of tshβb expression in April, concomitant with downstream migration initiation, while tshβa expression remained relatively constant. In situ hybridization showed two distinct pituitary cell populations, tshβa cells in the anterior adenohypophysis, and tshβb cells near to the pituitary stalk, a location comparable to the pars tuberalis TSH cells involved in seasonal physiology and behaviour in birds and mammals. Functional divergence of tshβ paralogs in Atlantic salmon supports a specific role of tshβb in smoltification.
DNA DSB Repair Dynamics following Irradiation with Laser-Driven Protons at Ultra-High Dose Rates
Authors: Hanton F. , Chaudhary P. , Doria D. , Gwynne D. , Maiorino C. , Scullion C. , Ahmed H. , Marshall T. , Naughton K. , Romagnani L. , Kar S. , Schettino G. , McKenna P. , Botchway S. , Symes D. R. , Rajeev P. P. , Prise K. M. , Borghesi M.
Published: March 2019

Protontherapy has emerged as more effective in the treatment of certain tumors than photon based therapies. However, significant capital and operational costs make protontherapy less accessible. This has stimulated interest in alternative proton delivery approaches, and in this context the use of laser-based technologies for the generation of ultra-high dose rate ion beams has been proposed as a prospective route. A better understanding of the radiobiological effects at ultra-high dose-rates is important for any future clinical adoption of this technology. In this study, we irradiated human skin fibroblasts-AG01522B cells with laser-accelerated protons at a dose rate of 109 Gy/s, generated using the Gemini laser system at the Rutherford Appleton Laboratory, UK. We studied DNA double strand break (DSB) repair kinetics using the p53 binding protein-1(53BP1) foci formation assay and observed a close similarity in the 53BP1 foci repair kinetics in the cells irradiated with 225 kVp X-rays and ultra- high dose rate protons for the initial time points. At the microdosimetric scale, foci per cell per track values showed a good correlation between the laser and cyclotron-accelerated protons indicating similarity in the DNA DSB induction and repair, independent of the time duration over which the dose was delivered.
Circadian and wake-dependent changes in human plasma polar metabolites during prolonged wakefulness: A preliminary analysis
Authors: Grant Leilah K. , Ftouni Suzanne , Nijagal Brunda , De Souza David P. , Tull Dedreia , McConville Malcolm J. , Rajaratnam Shantha M. W. , Lockley Steven W. , Anderson Clare
Published: March 2019

Establishing circadian and wake-dependent changes in the human metabolome are critical for understanding and treating human diseases due to circadian misalignment or extended wake. Here, we assessed endogenous circadian rhythms and wake-dependent changes in plasma metabolites in 13 participants (4 females) studied during 40-hours of wakefulness. Four-hourly plasma samples were analyzed by hydrophilic interaction liquid chromatography (HILIC)-LC-MS for 1,740 metabolite signals. Group-averaged (relative to DLMO) and individual participant metabolite profiles were fitted with a combined cosinor and linear regression model. In group-level analyses, 22% of metabolites were rhythmic and 8% were linear, whereas in individual-level analyses, 14% of profiles were rhythmic and 4% were linear. We observed metabolites that were significant at the group-level but not significant in a single individual, and metabolites that were significant in approximately half of individuals but not group-significant. Of the group-rhythmic and group-linear metabolites, only 7% and 12% were also significantly rhythmic or linear, respectively, in ≥50% of participants. Owing to large inter-individual variation in rhythm timing and the magnitude and direction of linear change, acrophase and slope estimates also differed between group- and individual-level analyses. These preliminary findings have important implications for biomarker development and understanding of sleep and circadian regulation of metabolism.
Role of Low-Affinity Calcium System Member Fig1 Homologous Proteins in Conidiation and Trap-Formation of Nematode-trapping Fungus Arthrobotrys oligospora
Authors: Zhang Weiwei , Hu Chengcheng , Hussain Muzammil , Chen Jiezuo , Xiang Meichun , Liu Xingzhong
Published: March 2019

Arthrobotrys oligospora is a typical nematode-trapping fungus capturing free-living nematodes by adhesive networks. Component of the low-affinity calcium uptake system (LACS) has been documented to involve in growth and sexual development of filamentous fungi. Bioassay showed incapacity of trap formation in A. oligospora on Water Agar plate containing 1 mM ethylene glycol tetraacetic acid (EGTA) due to Ca2+ absorbing block. The functions of homologous proteins (AoFIG_1 and AoFIG_2) of LACS were examined on conidiation and trap formation of A. oligospora. Compared with wild type, ΔAoFIG_1 (AOL_s00007g566) resulted in 90% of trap reduction, while ΔAoFIG_2 (AOL_s00004g576) reduced vegetative growth rate up to 44% and had no trap and conidia formed. The results suggest that LACS transmembrane protein fig1 homologs play vital roles in the trap-formation and is involved in conidiation and mycelium growth of A. oligospora. Our findings expand fig1 role to include development of complex trap device and conidiation.