Miracle-dz/UniFAR-FTUs huggingface dataset:
Equipped for Migrations Across High Latitude Regions? Reduced Spur Length and Outcrossing Rate in a Biennial Halenia elliptica (Gentianaceae) With Mixed Mating System Along a Latitude Gradient

Halenia (Gentianaceae) originated from the mountain regions of East Asia, and diversified in America following long migrations via Beringia. While Halenia elliptica, one species of the genus in China, migrated toward high latitudes in China. Spur length of H. elliptica is highly variable. We examined the relationship between spur length and mating pattern along a latitude gradient. Field experiments were performed in two populations of H. elliptica, and we found that this species could produce seeds via both autonomous selfing and the aid of pollinators, suggesting a mixed mating system. In seven populations of H. elliptica along a latitudinal gradient, we found a trend of decrease in spur length with the increase of latitude. Based on molecular data from 11 microsatellite loci, we found that multilocus outcrossing rate decreased with the increase of latitude while the estimated inbreeding depression increased significantly, indicating that a high degree of inbreeding depression might have prevented evolution toward complete selfing in the high latitude populations with short spur length, and thus maintained mixed mating system of H. elliptica. Our results suggest that the mixed mating system of this species might be helpful in overcoming pollinator scarcity in newly colonized populations toward high latitudes after its origination in the mountain regions of China, and the decrease of spur length in the high latitude populations could result from reduced resource allocation to pollinator associated traits.
Zika Virus Non-structural Protein 4A Blocks the RLR-MAVS Signaling

Flaviviruses have evolved complex mechanisms to evade the mammalian host immune systems including the RIG-I (retinoic acid-inducible gene I) like receptor (RLR) signaling. Zika virus (ZIKV) is a re-emerging flavivirus that is associated with severe neonatal microcephaly and adult Guillain-Barre syndrome. However, the molecular mechanisms underlying ZIKV pathogenesis remain poorly defined. Here we report that ZIKV non-structural protein 4A (NS4A) impairs the RLR-mitochondrial antiviral-signaling protein (MAVS) interaction and subsequent induction of antiviral immune responses. In human trophoblasts, both RIG-I and melanoma differentiation-associated protein 5 (MDA5) contribute to type I interferon (IFN) induction and control ZIKV replication. Type I IFN induction by ZIKV is almost completely abolished in MAVS-/- cells. NS4A represses RLR-, but not Toll-like receptor-mediated immune responses. NS4A specifically binds the N-terminal caspase activation and recruitment domain (CARD) of MAVS and thus blocks its accessibility by RLRs. Our study provides in-depth understanding of the molecular mechanisms of immune evasion by ZIKV and its pathogenesis.
Response of water use efficiency to summer drought in a boreal Scots pine forest in Finland

Abstract. The influence of drought on plant functioning has received considerable attention in recent years, however our understanding of the response of carbon and water coupling to drought in terrestrial ecosystems still needs to be improved. A severe soil moisture drought occurred in southern Finland in the late summer of 2006. In this study, we investigated the response of water use efficiency to summer drought in a boreal Scots pine forest (Pinus sylvestris) on the daily time scale mainly using eddy covariance flux data from the Hyytiala (southern Finland) flux site. In addition, simulation results from the JSBACH land surface model were evaluated against the observed results. Based on observed data, the ecosystem level water use efficiency (EWUE; the ratio of gross primary production, GPP, to evapotranspiration, ET) showed a decrease during the severe soil moisture drought, while the inherent water use efficiency (IWUE; a quantity defined as EWUE multiplied with mean daytime vapour pressure deficit, VPD) increased and the underlying water use efficiency (uWUE, a metric based on IWUE and a simple stomatal model, is the ratio of GPP multiplied with a square root of VPD to ET) was unchanged during the drought. The decrease in EWUE was due to the stronger decline in GPP than in ET. The increase in IWUE was because of the decreased stomatal conductance under increased VPD. The unchanged uWUE indicates that the trade-off between carbon assimilation and transpiration of the boreal Scots pine forest was not disturbed by this drought event at the site. The JSBACH simulation showed declines of both GPP and ET under the severe soil moisture drought, but to a smaller extent compared to the observed GPP and ET. Simulated GPP and ET led to a smaller decrease in EWUE but a larger increase in IWUE because of the severe soil moisture drought in comparison to observations. As in the observations, the simulated uWUE showed no changes in the drought event. The model deficiencies exist mainly due to the lack of the limiting effect of increased VPD on stomatal conductance during the low soil moisture condition. Our study provides a deeper understanding of the coupling of carbon and water cycles in the boreal Scots pine forest ecosystem and suggests possible improvements to land surface models, which play an important role in the prediction of biosphere–atmosphere feedbacks in the climate system.
From emissions to ambient mixing ratios: online seasonal field measurements of volatile organic compounds over a Norway spruce-dominated forest in central Germany

Biogenic volatile organic compounds (BVOCs) are substantial contributors to atmospheric chemistry and physics and demonstrate the close relationship between bio- sphere and atmosphere. Their emission rates are highly sensi- tive to meteorological and environmental changes with con- comitant impacts on atmospheric chemistry. We have inves- tigated seasonal isoprenoid and oxygenated VOC (oxVOC) fluxes from a Norway spruce ( Picea abies) tree in central Germany and explored the emission responses under various atmospheric conditions. Emission rates were quantified by using dynamic branch enclosure and proton-transfer-reaction mass spectrometry (PTR-MS) techniques. Additionally, am- bient mixing ratios were derived through application of a new box model treatment on the dynamic chamber measure- ments. These are compared in terms of abundance and ori- gin with the corresponding emissions. Isoprenoids dominate the BVOC emissions from Norway spruce, with monoter- penes and sesquiterpenes accounting for 50.8± 7.2 % and 19.8± 8.1 % respectively of the total emissions. Normalizing the VOC emission rates, we have observed a trend of reduc- tion of carbon-containing emissions from April to Novem- ber, with an enhancement of oxVOC. Highest emission rates were observed in June for all measured species, with the ex- ception of sesquiterpenes, which were emitted most strongly in April. Finally, we evaluate the temperature-dependent al- gorithm that seems to describe the temperature-dependent emissions of methanol, acetaldehyde and monoterpenes but only with the use of the monthly derived values for emission potential, Es, and temperature dependency, factor.
Response to Comment on Redondo et al. Racial/Ethnic Minority Youth With Recent-Onset Type 1 Diabetes Have Poor Prognostic Factors. Diabetes Care 2018;41:1017–1024

We thank Dr. Nwosu for his thoughtful comments (1). We agree that insulin resistance influences insulin dose–adjusted hemoglobin A1c (IDAA1c). Nagl et al. (2) observed that the partial remission period was less frequent and shorter in girls than boys, but, without C-peptide measurements, the authors could only speculate that higher insulin resistance or lower insulin secretion might explain their findings. However, we found that, adjusting for BMI, age, and sex, insulin doses were still different between African Americans (AAs) and non-Hispanic whites (NHWs) ( P < 0.001) (3), suggesting that after controlling for factors that increase insulin resistance there was still a difference in insulin dose, and thus in IDAA1c. Other measures of partial remission period, e.g., insulin dose, are also affected by insulin resistance. Furthermore, although defining partial remission period based on …
Do Actomyosin Single-Molecule Mechanics Data Predict Mechanics of Contracting Muscle?

In muscle, but not in single-molecule mechanics studies, actin, myosin and accessory proteins are incorporated into a highly ordered myofilament lattice. In view of this difference we compare results from single-molecule studies and muscle mechanics and analyze to what degree data from the two types of studies agree with each other. There is reasonable correspondence in estimates of the cross-bridge power-stroke distance (7–13 nm), cross-bridge stiffness (~2 pN/nm) and average isometric force per cross-bridge (6–9 pN). Furthermore, models defined on the basis of single-molecule mechanics and solution biochemistry give good fits to experimental data from muscle. This suggests that the ordered myofilament lattice, accessory proteins and emergent effects of the sarcomere organization have only minor modulatory roles. However, such factors may be of greater importance under e.g., disease conditions. We also identify areas where single-molecule and muscle data are conflicting: (1) whether force generation is an Eyring or Kramers process with just one major power-stroke or several sub-strokes; (2) whether the myofilaments and the cross-bridges have Hookean or non-linear elasticity; (3) if individual myosin heads slip between actin sites under certain conditions, e.g., in lengthening; or (4) if the two heads of myosin cooperate.
The Antitumor Immunity Mediated by NK Cells: The Role of The NCRs

Natural Killer (NK) cells are innate immune lymphocytes that are important for early and effective immune responses against infections and cancer. The antitumor immunity mediated by NK cells can be exerted through several direct or indirect “immunosurveillance” mechanisms that control tumor growth and prevent the rapid dissemination of metastatic tumors. NK cells express an array of activating and inhibitory receptors that enable them to recognize and bind non-self as well as self-ligands expressed on the surface of malignant or virally infected cells. The family of Natural Cytotoxicity Receptors (NCRs) comprises three activating receptors; NKp30, NKp44, and NKp46 that are important for the stimulation of NK cell effector functions. This review summarizes the mechanisms of antitumor immunity mediated by natural killer cells with focus on the role of the family of the NCRs and their tumor associated ligands.
Regional Dominant Frequency: A New Tool for Wave Break Identification During Atrial Fibrillation

Cardiac mapping systems are based on the time/frequency feature analyses of intracardiac electrograms recorded from individual bipolar/unipolar electrodes. Signals from each electrode are processed independently. Such approaches fail to investigate the interrelationship between simultaneously recorded channels of any given mapping catheter during atrial fibrillation (AF). We introduce a novel signal processing technique that reflects regional dominant frequency (RDF) components. We show that RDF can be used to identify and characterize variation and disorganization in wavefront propagation- wave breaks. The intracardiac electrograms from the left atrium of 15 patients were exported to MATLAB and custom software employed to estimate RDF and wave break rate (WBR). We observed a heterogeneous distribution of both RDF and WBR; the two measures were weakly correlated (0.3; p < 0.001). We identified locations of AF or atrial tachycardia (ATach) termination and later compared offline with RDF and WBR maps. We inspected our novel metrics for associations with AF termination sites. Areas associated with AF termination demonstrated high RDF and low WBR (↑RDF,↓WBR). These sites were present in 14 of 15 patients (mean 2.6 ± 1.2 sites per patient; range, 1–4 sites), 43% situated within the pulmonary veins. In nine patients where AF terminated to sinus rhythm (6) or ATach (3), post-hoc analysis demonstrated all ↑RDF,↓WBR sites were ablated and correlated with AF termination sites. The proposed RDF signal processing tools can be used to identify and quantify wave break, and the combined use of these two novel metrics can aid characterization of AF. Further prospective studies are warranted.
Indexed Lawvere theories for local state

Monads for global state and local state have been used to provide semantics of programming languages for many years. There is a computation- ally natural presentation of an ordinary Lawvere theory that corresponds to the monad on Set for global state, inevitably called the Lawvere theory for global state. Here, we introduce a notion of indexed Lawvere theory and use it to give a Lawvere-style account of local state, extending the theorem for global state to local state. En route, we develop the notion of comodel of a Lawvere theory and exploit a universal characterisation of the category of worlds for local state. Ultimately, we give both syntactic and semantic characterisations of the operation block that allows one to move between worlds and use them to characterise the monad for local state.
Nitrogen oxides and ozone fluxes from an oilseed-rape management cycle: the influence of cattle slurry application

Abstract. This study reports NO, NO2 and O3 mixing ratios and flux measurements using the eddy covariance method during a 7-month period over an oilseed-rape field, spanning an organic and a mineral fertilisation event. Cumulated NO emissions during the whole period were in agreement with previous studies and showed quite low emissions of 0.26 kg N ha−1 with an emission factor of 0.27 %, estimated as the ratio between total N emitted in the form of NO and total N input. The NO emissions were higher following organic fertilisation in August due to conditions favouring nitrification (soil water content around 20 % and high temperatures), while mineral fertilisation in February did not result in high emissions. The ozone deposition velocity increased significantly after organic fertilisation. The analysis of the chemical and turbulent transport times showed that reactions between NO, NO2 and O3 below the measurement height occurred constantly throughout the 7-month period. Following organic fertilisation, the NO ground fluxes were 30 % larger than the NO fluxes at the measurement height (3.2 m), while the NO2 fluxes switched from deposition to emission during certain periods, being negative at the surface and positive at the measurement height. This phenomenon of apparent NO2 emissions appears to be significant during strong NO emissions and high O3 ambient mixing ratios, even on a bare soil during August.
Stability and Side Effects of Orthodontic Retainers - A Systematic Review

Background: The role of orthodontic retainers in maintaining stability after orthodontic treatment, and side effects associated with orthodontic retainers have not been well established. Objective: To investigate whether fixed retainers improve stability after orthodontic treatment, or increase the risk of side effects on the teeth and periodontium in comparison with removable retainers, no retainer, or fiberotomy. Methods: A systematic literature search was conducted in PubMed, Embase, the Cochrane Library, HTAdatabases of NHS Centre for Reviews and Dissemination, Swedish Council on Health Technology Assessment (SBU), Norwegian Knowledge Centre for the Health Services (NOKC), Danish Health and Medicines Authority, and reference lists. Data extraction was verified by at least two authors. The quality of evidence was rated. Meta-analysis was not suitable. Results: Two systematic reviews (SR), two randomized controlled trials (RCT), four non-randomized controlled studies (CT), and five case series were included. The SRs were well reported, but addressed issues that differed from the addressed question, or did not add to the identified primary studies. Both RCTs and CTs had study limitations, and problems with directness and/or precision. None of the studies compared fixed retainers to fiberotomy. Conclusion: According to the literature there is only low quality of evidence, that treatment stability may be improved by a fixed retainer after orthodontic treatment in comparison with a removable retainer, or no retainer (GRADE ⊕⊕ââ). Furthermore, there is very low quality of evidence, whether periodontal outcomes, dental caries prevalence, or presence of calculus differ between the various types of retainer regimens (GRADE ⊕âââ).
Surface-induced nonlinearity enhancement in subwavelength rod waveguides

We develop a perturbative theory to describe optical propagation in subwavelength rod waveguides. In this approach, we account for loss and nonlinearity in the boundary conditions. A comparison to the traditional perturbative approach used in optical fibers reveals that the surface contribution provides a significant nonlinearity enhancement in the subwavelength regime. We further compare the nonlinearity enhancement of metallic, dielectric, and semiconductor waveguides, in addition to determining the attenuation coefficient of metallic nanowires.
Physicochemical Characterization of Sediment in Northwest Arkansas Streams

Eutrophication of surface waters is a critical concern in regions around the world facing nutrient surpluses as a result of confined animal feeding operations (CAFOs) and subsequent land application of manures. While large amounts of research exist on the transport of nutrient enriched runoff from fields to surface waters less information is available on in-stream processes controlling the transport of P in-stream. Thus, information is needed on the role of stream sediments in regulating transient phosphorus (P) to better understand the relationship between nutrient inputs and water quality. Fine-sized sediments ( 2-mm) consume and store P. From fine-sized sediment a modified P saturation ratio (PSRmod), related to the sediment’s ability to bind P and determined from Mehlich-3 extracted nutrients, has been correlated to in-stream dissolved reactive P (DRP) concentrations. The objectives of this study were to determine the relative size distribution of total- and fine-sized sediment (sand, silt clay) fractions among streams, determine the optimum sample number needed to characterize Mehlich-3 P (M3P) and PSRmod, and finally determine the applicability of PSRmod, as an indicator of stream water column DRP concentrations. Stream sediments were sampled from the 0- to 3-cm depth from stream reaches ranging from (25 – 75 m) in August, 2008 for characterization along with water samples collected from the thalweg for DRP concentration determination. Additional water column samples were collected along with fine-sized sedi- ment chemical properties in February, May, and June 2009. The distribution of sediment size classes was statistically similar, with 2- to 20- and 20- to 75-mm sized sediment dominating. Fine-sized sediment (mod, were determined to typically be sufficiently characterized by a sample scheme utilizing three samples points. Modified P saturation ratio of mod, has the potential to be used as an indicator of the ability of stream sediments to enrich stream water with P. Thus, fine-sized sediment nutrient concentrations appear to be key regulators of water column P concentrations.
Semi-Automated Method for Multi-Tasking Measurement of Microbial Growth, Capsule, and Biofilm Formation

The majority of bacterial infections involve the formation of biofilms. Biofilm formation is nutrient and growth dependent. Determination of the effects of nutrients on exopolysaccharide production and bacterial growth is labor and time intensive. We tested whether the Bioscreen C (Growth Curves, Inc.) would have utility as a high-throughput tool in the measurement of fundamental phenotype expression, as it relates to growth conditions. Within 48 - 72 hr, reproduceble, statistically significant data on the affects of growth conditions on generation time, capsule production and biofilm formation (maximally for 25 different conditions per 24 hr run cycle; n = 4) were obtained. Although all S. aureus strains produced similar amounts of capsule, sarA– and agr– strains grew significantly slower than parent strain (1.6 fold slower) and produced significantly (p 0.05) less biofilm (~2 fold). E. coli growth rate, biofilm and capsule production in simulated nephropathic urine medium was similar for urine with insulin (20 μU). Addition of insulin to urine medium with proline increased generation time, capsule and biofilm production. Findings from this study show that the Bioscreen C is a rapid, reproducible, and easily manipulated system to concurrently measure bacterial growth, biofilm formation, and capsule production. In addition, there is the potential for further applications of this system by expanding the types of detector dyes used.
Virtual Codec Supervised Re-Sampling Network for Image Compression

In this paper, we propose an image re-sampling compression method by learning virtual codec network (VCN) to resolve the non-differentiable problem of quantization function for image compression. Here, the image re-sampling not only refers to image full-resolution re-sampling but also low-resolution re-sampling. We generalize this method for standard-compliant image compression (SCIC) framework and deep neural networks based compression (DNNC) framework. Specifically, an input image is measured by re-sampling network (RSN) network to get re-sampled vectors. Then, these vectors are directly quantized in the feature space in SCIC, or discrete cosine transform coefficients of these vectors are quantized to further improve coding efficiency in DNNC. At the encoder, the quantized vectors or coefficients are losslessly compressed by arithmetic coding. At the receiver, the decoded vectors are utilized to restore input image by image decoder network (IDN). In order to train RSN network and IDN network together in an end-to-end fashion, our VCN network intimates projection from the re-sampled vectors to the IDN-decoded image. As a result, gradients from IDN network to RSN network can be approximated by VCN network's gradient. Because dimension reduction can be further achieved by quantization in some dimensional space after image re-sampling within auto-encoder architecture, we can well initialize our networks from pre-trained auto-encoder networks. Through extensive experiments and analysis, it is verified that the proposed method has more effectiveness and versatility than many state-of-the-art approaches.