bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT: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.
Unusually variable paleocommunity composition in the oldest metazoan fossil assemblages
Authors: Finnegan Seth , Gehling James G. , Droser Mary L. 
Published: March 2019

AbstractRecent 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

AbstractCarolina 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

AbstractFor 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.
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

AbstractOptical 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

AbstractEfficient 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

AbstractSparse 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

AbstractPhenotypically 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

AbstractPeptidomics 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

AbstractSignaling 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

AbstractPatients 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

AbstractSupercontinuum (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

AbstractAnomalous 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

AbstractTemperature 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

AbstractWild 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.