bluuebunny/crossref_metadata_2025_split huggingface dataset:
Processes and facies relationships in a Lower(?) Devonian rocky shoreline depositional environment, East Lime Creek Conglomerate, south‐western Colorado, USA
Authors: Evans James E. , Holm‐Denoma Christopher S. 
Published: February 2018

AbstractRocky shorelines are relatively common features along modern coastlines, but few have been recognized in the geological record. The hard substrates of rocky shorelines telescope the width of offshore marine environments, thus the diagnostic deposits observed in such settings today have a low preservation potential due to small accommodation space and high‐energy conditions. This study recognized previously overlooked, laterally extensive Lower(?) Devonian rocky shoreline deposits in the San Juan Mountains of south‐western Colorado. The newly defined lithostratigraphic unit, the East Lime Creek Conglomerate (ELCC), is 0–23 m thick, unconformably overlying Proterozoic crystalline rocks and unconformably overlain by the Upper Devonian Ignacio Formation and/or Elbert Formation. The unit mostly consists of clast‐supported cobble‐boulder conglomerate with rounded quartzite clasts up to 1.4 m in length interbedded with thin sandstone layers and lenses. Sandstones in the ELCC are distinguished from unconformably overlying Upper Devonian sedimentary rocks because they have sericite cements. Most importantly, there are buttressing relationships between the ELCC and underlying Proterozoic crystalline rocks interpreted as palaeo‐sea cliffs, palaeo‐wave‐cut platforms and palaeo‐tombolos. A proposed rocky shoreline facies model includes headlands with upper shoreface‐beachface tabular cobble‐boulder gravels sourced from rock fall talus, nearshore subaqueous debris‐flow deposits and intervening pocket beaches with imbricated, stratified pebble‐cobble gravel sheets. Palaeocurrent data (n = 338) from clast long‐axis orientations, imbrication and cross‐bedding indicate south‐to‐north transport roughly onshore‐offshore to a coastline consisting of alternating rocky headlands and pocket beaches. This Lower(?) Devonian unit documents a previously unrecognized episode in the geological history of south‐western Colorado.
An analytical framework for estimating aquatic species density from environmental DNA
Authors: Chambert Thierry , Pilliod David S. , Goldberg Caren S. , Doi Hideyuki , Takahara Teruhiko 
Published: February 2018

AbstractEnvironmental DNA (eDNA) analysis of water samples is on the brink of becoming a standard monitoring method for aquatic species. This method has improved detection rates over conventional survey methods and thus has demonstrated effectiveness for estimation of site occupancy and species distribution. The frontier of eDNA applications, however, is to infer species density. Building upon previous studies, we present and assess a modeling approach that aims at inferring animal density from eDNA. The modeling combines eDNA and animal count data from a subset of sites to estimate species density (and associated uncertainties) at other sites where only eDNA data are available. As a proof of concept, we first perform a cross‐validation study using experimental data on carp in mesocosms. In these data, fish densities are known without error, which allows us to test the performance of the method with known data. We then evaluate the model using field data from a study on a stream salamander species to assess the potential of this method to work in natural settings, where density can never be known with absolute certainty. Two alternative distributions (Normal and Negative Binomial) to model variability in eDNA concentration data are assessed. Assessment based on the proof of concept data (carp) revealed that the Negative Binomial model provided much more accurate estimates than the model based on a Normal distribution, likely because eDNA data tend to be overdispersed. Greater imprecision was found when we applied the method to the field data, but the Negative Binomial model still provided useful density estimates. We call for further model development in this direction, as well as further research targeted at sampling design optimization. It will be important to assess these approaches on a broad range of study systems.
Population genetic structure, introgression, and hybridization in the genus Rhizophora along the Brazilian coast
Authors: Francisco Patrícia M. , Mori Gustavo M. , Alves Fábio M. , Tambarussi Evandro V. , de Souza Anete P. 
Published: February 2018

AbstractMangrove plants comprise plants with similar ecological features that have enabled them to adapt to life between the sea and the land. Within a geographic region, different mangrove species share not only similar adaptations but also similar genetic structure patterns. Along the eastern coast of South America, there is a subdivision between the populations north and south of the continent's northeastern extremity. Here, we aimed to test for this north‐south genetic structure in Rhizophora mangle, a dominant mangrove plant in the Western Hemisphere. Additionally, we aimed to study the relationships between R. mangle, R. racemosa, and R. × harrisonii and to test for evidence of hybridization and introgression. Our results confirmed the north‐south genetic structure pattern in R. mangle and revealed a less abrupt genetic break in the northern population than those observed in Avicennia species, another dominant and widespread mangrove genus in the Western Hemisphere. These results are consistent with the role of oceanic currents influencing sea‐dispersed plants and differences between Avicennia and Rhizophora propagules in longevity and establishment time. We also observed that introgression and hybridization are relevant biological processes in the northeastern coast of South America and that they are likely asymmetric toward R. mangle, suggesting that adaptation might be a process maintaining this hybrid zone.
A generalist and a specialist herbivore are differentially affected by inbreeding and trichomes in Mimulus guttatus
Authors: Haber Ariela I. , Rivera Sustache Julia , Carr David E. 
Published: February 2018

AbstractInbreeding in plants is well known to affect plant–herbivore interactions, but these effects can depend on herbivore host breadth. If the phenotypic effects of inbreeding are analogous to those of environmental stress, the plant stress hypothesis predicts that generalist herbivores will perform better on inbred relative to outbred plants because inbreeding is expected to lower chemical defenses. The plant vigor hypothesis predicts that specialist herbivores will perform better on outbred relative to inbred plants because specialists are more tolerant of plant defenses and benefit from the higher nutritional quality of outbred plants. However, these plant defense theories do not account for structural defenses. Using a factorial design, we examined effects of inbreeding and trichome density in Mimulus guttatus on performance of the generalist, Helicoverpa zea, and the specialist, Junonia coenia. We also examined preferences of each herbivore for leaf disks and olfactory cues from inbred vs. outbred plants. The generalist H. zea developed most efficiently on inbred plants. The specialist J. coenia exhibited the greatest mass gain and pupal mass and developed fastest on outbred plants. Trichomes negatively affected performance of both species. Helicoverpa zea did not exhibit strong preferences for inbred vs. outbred plants, but J. coenia consistently preferred outbred plants. Our results support predictions on the effects of inbreeding on herbivore performance, but trichomes reduced performance of both herbivores. We conclude that the ability of the plant stress and plant vigor hypotheses to predict inbreeding effects on plant–herbivore interactions may depend on which plant traits are affected by inbreeding.
Arginase‐1 is neither constitutively expressed in nor required for myeloid‐derived suppressor cell‐mediated inhibition of T‐cell proliferation
Authors: Bian Zhen , Abdelaal Ahmed Mansour , Shi Lei , Liang Hongwei , Xiong Lanqiao , Kidder Koby , Venkataramani Mahathi , Culpepper Courtney , Zen Ke , Liu Yuan 
Published: February 2018

AbstractAlthough previous reports suggest that tumor‐induced myeloid‐derived suppressor cells (MDSC) inhibit T cells by L‐arginine depletion through arginase‐1 activity, we herein show that arginase‐1 is neither inherently expressed in MDSC nor required for MDSC‐mediated inhibition. Employing Percoll density gradients, large expansions of MDSC in the bone marrow of tumor‐bearing mice were isolated and demonstrated potent inhibition in T‐cell proliferation activated by TCR‐ligation, Concanavalin A, PMA plus ionomycin, or IL‐2. Despite demonstrating characteristic immunosuppressive capacity, these MDSC exhibit no arginase‐1 expression and/or exert their inhibitory effects independent of arginase‐1 activity. However, arginase‐1 expression in MDSC can be induced by exposure to TCR‐activated T cells or their culture medium, but not T cells activated by other means or growing tumor cells. Further investigation reveals multiple cytokines secreted by TCR‐activated T cells as orchestrating two signaling‐relay axes, IL‐6‐to‐IL‐4 and GM‐CSF/IL‐4‐to‐IL‐10, leading to arginase‐1 expression in MDSC. Specifically, IL‐6 signaling increases IL‐4R, enabling IL‐4 to induce arginase‐1 expression; similarly, GM‐CSF in concert with IL‐4 induces IL‐10R, allowing IL‐10‐mediated induction. Surprisingly, our study indicates that induction of arginase‐1 expression is not conducive to the critical MDSC‐mediated inhibition toward T cells, which is rather dependent on direct cell contacts undiminished by PD‐L1 blockade or SIRPα deficiency.
The influence of mindfulness, self‐compassion, psychological flexibility, and posttraumatic stress disorder on disability and quality of life over time in war veterans
Authors: Meyer Eric C. , Frankfurt Sheila B. , Kimbrel Nathan A. , DeBeer Bryann B. , Gulliver Suzy B. , Morrisette Sandra B. 
Published: February 2018

AbstractObjectivesPosttraumatic stress disorder (PTSD) strongly predicts greater disability and lower quality of life (QOL). Mindfulness‐based and other third‐wave behavior therapy interventions improve well‐being by enhancing mindfulness, self‐compassion, and psychological flexibility. We hypothesized that these mechanisms of therapeutic change would comprise a single latent factor that would predict disability and QOL after accounting for PTSD symptom severity.MethodIraq and Afghanistan war veterans (N = 117) completed a study of predictors of successful reintegration. Principal axis factor analysis tested whether mindfulness, self‐compassion, and psychological flexibility comprised a single latent factor. Hierarchical regression tested whether this factor predicted disability and QOL 1 year later.ResultsMindfulness, self‐compassion, and psychological flexibility comprised a single factor that predicted disability and QOL after accounting for PTSD symptom severity. PTSD symptoms remained a significant predictor of disability but not QOL.ConclusionsTargeting these mechanisms may help veterans achieve functional recovery, even in the presence of PTSD symptoms.
Identification and validation of a multi‐assay algorithm for cross‐sectional HIV incidence estimation in populations with subtype C infection
Authors: Laeyendecker Oliver , Konikoff Jacob , Morrison Douglas E , Brookmeyer Ronald , Wang Jing , Celum Connie , Morrison Charles S , Abdool Karim Quarraisha , Pettifor Audrey E , Eshleman Susan H 
Published: February 2018

AbstractIntroductionCross‐sectional methods can be used to estimate HIV incidence for surveillance and prevention studies. We evaluated assays and multi‐assay algorithms (MAAs) for incidence estimation in subtype C settings.MethodsWe analysed samples from individuals with subtype C infection with known duration of infection (2442 samples from 278 adults; 0.1 to 9.9 years after seroconversion). MAAs included 1‐4 of the following assays: Limiting Antigen Avidity assay (LAg‐Avidity), BioRad‐Avidity assay, CD4 cell count and viral load (VL). We evaluated 23,400 MAAs with different assays and assay cutoffs. We identified the MAA with the largest mean window period, where the upper 95% confidence interval (CI) of the shadow was <1 year. This MAA was compared to the LAg‐Avidity and BioRad‐Avidity assays alone, a widely used LAg algorithm (LAg‐Avidity <1.5 OD‐n + VL >1000 copies/mL), and two MAAs previously optimized for subtype B settings. We compared these cross‐sectional incidence estimates to observed incidence in an independent longitudinal cohort.ResultsThe optimal MAA was LAg‐Avidity <2.8 OD‐n + BioRad‐Avidity <95% + VL >400 copies/mL. This MAA had a mean window period of 248 days (95% CI: 218, 284), a shadow of 306 days (95% CI: 255, 359), and provided the most accurate and precise incidence estimate for the independent cohort. The widely used LAg algorithm had a shorter mean window period (142 days, 95% CI: 118, 167), a longer shadow (410 days, 95% CI; 318, 491), and a less accurate and precise incidence estimate for the independent cohort.ConclusionsAn optimal MAA was identified for cross‐sectional HIV incidence in subtype C settings. The performance of this MAA is superior to a testing algorithm currently used for global HIV surveillance.
Polyplex Particles Based on Comb‐Like Polyethylenimine/Poly(2‐ethyl‐2‐oxazoline) Copolymers: Relating Biological Performance with Morphology and Structure
Authors: Haladjova Emi , Halacheva Silviya , Momekova Denitsa , Moskova‐Doumanova Veselina , Topouzova‐Hristova Tanya , Mladenova Kirilka , Doumanov Jordan , Petrova Maria , Rangelov Stanislav 
Published: February 2018

AbstractThe present contribution is focused on feasibility of using comb‐like copolymers of polyethylenimine with poly(2‐ethyl‐2‐oxazoline) (LPEI‐comb‐PEtOx) with varying grafting densities and degrees of polymerization of PEI and PEtOx to deliver DNA molecules into cells. The copolymers form small and well‐defined particles at elevated temperatures, which are used as platforms for binding and condensing DNA. The electrostatic interactions between particles and DNA result in formation of sub‐100 nm polyplex particles of narrow size distribution and different morphology and structure. The investigated gene delivery systems exhibit transfection efficiency dependent on the copolymer chain topology, shape of the polyplex particles, and internalization pathway. Flow cytometry shows enhanced transfection efficiency of the polyplexes with elongated and ellipsoidal morphology. The preliminary biocompatibility study on a panel of human cell lines shows that pure copolymers and polyplexes thereof are practically devoid of cytotoxicity.
A Fast, Reversible, and Robust Gradient Nanocomposite Hydrogel Actuator with Water‐Promoted Thermal Response
Authors: Tan Yun , Wang Di , Xu Huaxiu , Yang Yang , An Wenli , Yu Lina , Xiao Zhixin , Xu Shimei 
Published: February 2018

AbstractPoly(N‐isopropylacrylamide)/Laponite (PNIPAM/Laponite) gradient nanocomposite hydrogel actuators are developed as temperature‐controlled actuators with excellent performance using a facile electrophoresis method. The actuators exhibit a rapid (20 s response time) and reversible response, as well as large deformation (bending angle of 231°), which is due to the graded forces generated by the thermo‐induced anisotropic shrinkage and extension of the gradient hydrogels. A good linear relationship is observed between the maximum bending angles and the corresponding temperatures for the actuators with fixed sizes. Moreover, the gradient hydrogel with high water content achieved larger actuation angles and shorter response time than the one with low water content, showing an interesting water‐promoted effect. Meanwhile, different types of actuators are designed to suit for more specific scenarios, and may be used for various applications, such as biosensing, artificial organization, and transportation of targeted objects.
Animal models of l‐dopa‐induced dyskinesia in Parkinson's disease
Authors: Cenci M. Angela , Crossman Alan R. 
Published: February 2018

ABSTRACTUnderstanding the biological mechanisms of l‐dopa‐induced motor complications is dependent on our ability to investigate these phenomena in animal models of Parkinson's disease. The most common motor complications consist in wearing‐off fluctuations and abnormal involuntary movements appearing when plasma levels of l‐dopa are high, commonly referred to as peak‐dose l‐dopa‐induced dyskinesia. Parkinsonian models exhibiting these features have been well‐characterized in both rodent and nonhuman primate species. The first animal models of peak‐dose l‐dopa‐induced dyskinesia were produced in monkeys lesioned with N‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) and treated chronically with l‐dopa to elicit choreic movements and dystonic postures. Seminal studies were performed in these models using both metabolic mapping and electrophysiological techniques, providing fundamental pathophysiological insights that have stood the test of time. A decade later, it was shown possible to reproduce peak‐dose l‐dopa‐induced dyskinesia in rats and mice rendered parkinsonian with nigrostriatal 6‐hydroxydopamine lesions. When treated with l‐dopa, these animals exhibit abnormal involuntary movements having both hyperkinetic and dystonic components. These models have enabled molecular‐ and cellular‐level investigations into the mechanisms of l‐dopa‐induced dyskinesia. A flourishing literature using genetically engineered mice is now unraveling the role of specific genes and neural circuits in the development of l‐dopa‐induced motor complications. Both non‐human primate and rodent models of peak‐dose l‐dopa‐induced dyskinesia have excellent construct validity and provide valuable tools for discovering therapeutic targets and evaluating potential treatments. © 2018 International Parkinson and Movement Disorder Society
In vivo hyperpolarization transfer in a clinical MRI scanner
Authors: von Morze Cornelius , Reed Galen D. , Larson Peder E. , Mammoli Daniele , Chen Albert P. , Tropp James , Van Criekinge Mark , Ohliger Michael A. , Kurhanewicz John , Vigneron Daniel B. , Merritt Matthew E. 
Published: February 2018

PurposeThe purpose of this study was to investigate the feasibility of in vivo 13C‐>1H hyperpolarization transfer, which has significant potential advantages for detecting the distribution and metabolism of hyperpolarized 13C probes in a clinical MRI scanner.MethodsA standalone pulsed 13C RF transmit channel was developed for operation in conjunction with the standard 1H channel of a clinical 3T MRI scanner. Pulse sequences for 13C power calibration and polarization transfer were programmed on the external hardware and integrated with a customized water‐suppressed 1H MRS acquisition running in parallel on the scanner. The newly developed RF system was tested in both phantom and in vivo polarization transfer experiments in 1JCH‐coupled systems: phantom experiments in thermally polarized and hyperpolarized [2‐13C]glycerol, and 1H detection of [2‐13C]lactate generated from hyperpolarized [2‐13C]pyruvate in rat liver in vivo.ResultsOperation of the custom pulsed 13C RF channel resulted in effective 13C‐>1H hyperpolarization transfer, as confirmed by the characteristic antiphase appearance of 1H‐detected, 1JCH‐coupled doublets. In conjunction with a pulse sequence providing 190‐fold water suppression in vivo, 1H detection of hyperpolarized [2‐13C]lactate generated in vivo was achieved in a rat liver slice.ConclusionThe results show clear feasibility for effective 13C‐>1H hyperpolarization transfer in a clinical MRI scanner with customized heteronuclear RF system.
Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions
Authors: Yin Jie , Gosney Michael J. , Dilkes Brian P. , Mickelbart Michael V. 
Published: February 2018

AbstractEutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profiling and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome, and 65 of which were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long‐chain fatty acid derivatives as compared to SH, whereas sugars are more abundant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F1 hybrids than the mid‐parent averages and the accumulation of 17% of the metabolites in F1 plants transgressed the level in both parents. Concentrations of several metabolites in F1 hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of the E. salsugineum genome and newly identified high‐quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment.
High‐fidelity detection of crop biomass quantitative trait loci from low‐cost imaging in the field
Authors: Banan Darshi , Paul Rachel E. , Feldman Max J. , Holmes Mark W. , Schlake Hannah , Baxter Ivan , Jiang Hui , Leakey Andrew D.B. 
Published: February 2018

AbstractField‐based, rapid, and nondestructive techniques for assessing plant productivity are needed to accelerate the discovery of genotype‐to‐phenotype relationships in next‐generation biomass grass crops. The use of hemispherical imaging and light attenuation modeling was evaluated against destructive harvest measures with respect to their ability to accurately capture phenotypic and genotypic relationships in a field‐grown grass crop. Plant area index (PAI) estimated from below‐canopy hemispherical images, as well as a suite of thirteen traits assessed by manual destructive harvests, were measured in a Setaria recombinant inbred line mapping population segregating for aboveground productivity and architecture. A significant correlation was observed between PAI and biomass production across the population at maturity (r2 = .60), as well as for select diverse genotypes sampled repeatedly over the growing season (r2 = .79). Twenty‐seven quantitative trait loci (QTL) were detected for manually collected traits associated with biomass production. Of these, twenty‐one were found in four clusters of colocalized QTL. Analysis of image‐based estimates of PAI successfully identified all four QTL hot spots for biomass production. QTL for PAI had greater overlap with those detected for traits associated with biomass production than with those for plant architecture and biomass partitioning. Hemispherical imaging is an affordable and scalable method, which demonstrates how high‐throughput phenotyping can identify QTL related to biomass production of field trials in place of destructive harvests that are labor, time, and material intensive.