Miracle-dz/UniFAR-FTUs huggingface dataset:
The relationship between oesophageal heating during left atrial posterior wall ablation and the durability of pulmonary vein isolation

Aim During ablation of the posterior wall (PW), luminal oesophageal temperature elevation (OTE) prompts attenuation of radiofrequency (RF) energy delivery to minimize oesophageal injury. This strategy on lesion efficacy is unknown. The goal of this study was to analyse the relationship between OTE and pulmonary vein reconnection (PVR). Methods and results During the index antral pulmonary vein (PV) isolation procedure with an irrigated RF ablation catheter, OTE was detected with a multisensor oesophageal temperature probe. Posterior wall ablation did not exceed 25 W and was terminated when the temperature was ≥38.5°C. Patients undergoing redo procedures (n = 142) were studied for PW sites of PVR along 4 segments: left and right superior, and left and right inferior. Pulmonary vein reconnections had occurred in 51 of the 142 patients (36%), in 58 of 284 PV pairs (20%). Among these 58 reconnected pairs, 83% (n = 48) were along the PW. Oesophageal temperature elevation had occurred in 30 patients (59%). No difference in characteristics was seen between the patients with OTE (n = 30) and those without (n = 21). For superior segments, there was no interaction between the presence or absence of OTE and PVR. For inferior segments, there were more PVRs in the group with OTE: for the right-inferior segment, the PVR rate was 72% for OTE cases vs. 42% without (P = 0.04), and for the left-inferior segment, the PVR rate was 44% for OTE cases vs. 22.9% without (P = 0.12). Conclusion Pulmonary vein reconnections are predominantly posteriorly located. Along the right- and left-inferior PW segments, there was an association with elevated oesophageal temperature during the index procedure.
Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue

Metabolic homeostasis requires coordination between circadian clocks in different tissues. Also, systemic signals appear to be required for some transcriptional rhythms in the mammalian liver and the Drosophila fat body. Here we show that free-running oscillations of the fat body clock require clock function in the PDF-positive cells of the fly brain. Interestingly, rhythmic expression of the cytochrome P450 transcripts, sex-specific enzyme 1 (sxe1) and Cyp6a21, which cycle in the fat body independently of the local clock, depends upon clocks in neurons expressing neuropeptide F (NPF). NPF signaling itself is required to drive cycling of sxe1 and Cyp6a21 in the fat body, and its mammalian ortholog, Npy, functions similarly to regulate cycling of cytochrome P450 genes in the mouse liver. These data highlight the importance of neuronal clocks for peripheral rhythms, particularly in a specific detoxification pathway, and identify a novel and conserved role for NPF/Npy in circadian rhythms. DOI: http://dx.doi. org/10.7554/eLife.13552. 001
An update of the WCRF/AICR systematic literature review and meta-analysis on dietary and anthropometric factors and esophageal cancer risk

Abstract Background In the 2007 World Cancer Research Fund/American Institute for Cancer Research Second Expert Report, the expert panel judged that there was strong evidence that alcoholic drinks and body fatness increased esophageal cancer risk, whereas fruits and vegetables probably decreased its risk. The judgments were mainly based on case–control studies. As part of the Continuous Update Project, we updated the scientific evidence accumulated from cohort studies in this topic. Methods We updated the Continuous Update Project database up to 10 January 2017 by searching in PubMed and conducted dose–response meta-analyses to estimate summary relative risks (RRs) and 95% confidence intervals (CIs) using random effects model. Results A total of 57 cohort studies were included in 13 meta-analyses. Esophageal adenocarcinoma risk was inversely related to vegetable intake (RR per 100 g/day: 0.89, 95% CI: 0.80–0.99, n = 3) and directly associated with body mass index (RR per 5 kg/m2: 1.47, 95% CI: 1.34–1.61, n = 9). For esophageal squamous cell carcinoma, inverse associations were observed with fruit intake (RR for 100 g/day increment: 0.84, 95% CI: 0.75–0.94, n = 3) and body mass index (RR for 5 kg/m2 increment: 0.64, 95% CI: 0.56–0.73, n = 8), and direct associations with intakes of processed meats (RR for 50 g/day increment: 1.59, 95% CI: 1.11–2.28, n = 3), processed and red meats (RR for 100 g/day increment: 1.37, 95% CI: 1.04–1.82, n = 3) and alcohol (RR for 10 g/day increment: 1.25, 95% CI: 1.12–1.41, n = 6). Conclusions Evidence from cohort studies suggested a protective role of vegetables and body weight control in esophageal adenocarcinomas development. For squamous cell carcinomas, higher intakes of red and processed meats and alcohol may increase the risk, whereas fruits intake may play a protective role.
Reliability of Measuring Ileo-Colonic Disease Activity in Crohn's Disease by Magnetic Resonance Enterography.

Background Magnetic resonance enterography is increasingly utilized for assessment of luminal Crohn's disease activity. The Magnetic Resonance Index of Activity and the London Index are the most commonly used outcome measures in clinical trials. We assessed the reliability of these indices and several additional items. Methods A consensus process clarified scoring conventions and identified additional items based on face validity. Four experienced radiologists evaluated 50 images in triplicate, in random order, at least 1 month apart, using a central image management system. Intra- and interrater reliability were assessed by calculating and comparing intraclass correlation coefficients. Results Intrarater intraclass correlation coefficients (95% confidence intervals) for the Magnetic Resonance Index of Activity, London, and London "extended" indices and a visual analogue scale were 0.89 (0.84 to 0.91), 0.87 (0.83 to 0.90), 0.89 (0.85 to 0.92), and 0.86 (0.81 to 0.90). Corresponding interrater intraclass correlation coefficients were 0.71 (0.61 to 0.77), 0.67 (0.55 to 0.75), 0.70 (0.61 to 0.76), and 0.71 (0.62 to 0.77). Reliability for each index was greatest in the terminal ileum and poorest in the rectum. All 3 indices were highly correlated with the visual analogue scale; 0.79 (0.71 to 0.85), 0.78 (0.71 to 0.84), and 0.79 (0.72 to 0.85) for the Magnetic Resonance Index of Activity, London, and the London "extended" indices, respectively. Conclusions "Substantial" interrater reliability was observed for all 3 indices. Future studies should assess responsiveness to treatment in order to confirm their utility as evaluative indices in clinical trials and clinical practice.
No Difference between the Sexes in Fine-Scale Spatial Genetic Structure of Roe Deer

Background Data on spatial genetic patterns may provide information about the ecological and behavioural mechanisms underlying population structure. Indeed, social organization and dispersal patterns of species may be reflected by the pattern of genetic structure within a population. Methodology/Principal Findings We investigated the fine-scale spatial genetic structure of a roe deer (Capreolus capreolus) population in Trois-Fontaines (France) using 12 microsatellite loci. The roe deer is weakly polygynous and highly sedentary, and can form matrilineal clans. We show that relatedness among individuals was negatively correlated with geographic distance, indicating that spatially proximate individuals are also genetically close. More unusually for a large mammalian herbivore, the link between relatedness and distance did not differ between the sexes, which is consistent with the lack of sex-biased dispersal and the weakly polygynous mating system of roe deer. Conclusions/Significance Our results contrast with previous reports on highly polygynous species with male-biased dispersal, such as red deer, where local genetic structure was detected in females only. This divergence between species highlights the importance of socio-spatial organization in determining local genetic structure of vertebrate populations.
Vehicle Trajectory Prediction by Integrating Physics- and Maneuver-Based Approaches Using Interactive Multiple Models

Vehicle trajectory prediction helps automated vehicles and advanced driver-assistance systems have a better understanding of traffic environment and perform tasks such as criticality assessment in advance. In this study, an integrated vehicle trajectory prediction method is proposed by combining physics- and maneuver-based approaches. These two methods were combined for the reason that the physics-based trajectory prediction method could ensure accuracy in the short term with the consideration of vehicle running dynamic parameters, and the maneuver-based prediction approach has a long-term insight into future trajectories with maneuver estimation. In this study, the interactive multiple model trajectory prediction (IMMTP) method is proposed by combining the two predicting models. The probability of each model in the interactive multiple models could recursively adjust according to the predicting variance of each model. In addition, prediction uncertainty is considered by employing unscented Kalman filters in the physics-based prediction model. To the maneuver-based method, random elements for uncertainty are introduced to the trajectory of each maneuver inferred by using the dynamic Bayesian network. The approach is applied and analyzed in the lane-changing scenario by using naturalistic driving data. Comparison results indicate that IMMTP could achieve a more accurate prediction trajectory with a long prediction horizon.
Upper Ocean Response to Typhoon Kalmaegi and Sarika in the South China Sea from Multiple-Satellite Observations and Numerical Simulations

We investigated ocean surface and subsurface physical responses to Typhoons Kalmaegi and Sarika in the South China Sea, utilizing synergistic multiple-satellite observations, in situ measurements, and numerical simulations. We found significant typhoon-induced sea surface cooling using satellite sea surface temperature (SST) observations and numerical model simulations. This cooling was mainly caused by vertical mixing and upwelling. The maximum amplitudes were 6 °C and 4.2 °C for Typhoons Kalmaegi and Sarika, respectively. For Typhoon Sarika, Argo temperature profile measurements showed that temperature response beneath the surface showed a three-layer vertical structure (decreasing-increasing-decreasing). Satellite salinity observations showed that the maximum increase of sea surface salinity (SSS) was 2.2 psu on the right side of Typhoon Sarika’s track, and the maximum decrease of SSS was 1.4 psu on the left. This SSS seesaw response phenomenon is related to the asymmetrical rainfall on both sides of the typhoon track. Acoustic Doppler Current Profilers measurements and numerical simulations both showed that subsurface current velocities rapidly increased as the typhoon passed, with peak increases of up to 1.19 m/s and 1.49 m/s. Typhoon-generated SST cooling and current velocity increases both exhibited a rightward bias associated with a coupling between typhoon wind-stress and mixed layer velocity.
Analysis of Permafrost Region Coherence Variation in the Qinghai-Tibet Plateau with a High-Resolution TerraSAR-X Image

The Qinghai–Tibet Plateau (QTP) is heavily affected by climate change and has been undergoing serious permafrost degradation due to global warming. Synthetic aperture radar interferometry (InSAR) has been a significant tool for mapping surface features or measuring physical parameters, such as soil moisture, active layer thickness, that can be used for permafrost modelling. This study analyzed variations of coherence in the QTP area for the first time with high-resolution SAR images acquired from June 2014 to August 2016. The coherence variation of typical ground targets was obtained and analyzed. Because of the effects of active-layer (AL) freezing and thawing, coherence maps generated in the Beiluhe permafrost area exhibits seasonal variation. Furthermore, a temporal decorrelation model determined by a linear temporal-decorrelation component plus a seasonal periodic-decorrelation component and a constant component have been proposed. Most of the typical ground targets fit this temporal model. The results clearly indicate that railways and highways can hold high coherence properties over the long term in X-band images. By contrast, mountain slopes and barren areas cannot hold high coherence after one cycle of freezing and thawing. The possible factors (vegetation, soil moisture, soil freezing and thawing, and human activity) affecting InSAR coherence are discussed. This study shows that high-resolution time series of TerraSAR-X coherence can be useful for understanding QTP environments and for other applications.
Upwelling and isolation in oxygen-depleted anticyclonic modewater eddies and implications for nitrate cycling

The temporal evolution of the physical and bio-geochemical structure of an oxygen-depleted anticyclonic modewater eddy is investigated over a 2-month period using high-resolution glider and ship data. A weakly stratified eddy core (squared buoyancy frequency N 2 ∼ 0.1 × 10 −4 s −2 ) at shallow depth is identified with a horizontal extent of about 70 km and bounded by maxima in N 2 . The upper N 2 maximum (3–5 × 10 −4 s −2 ) coincides with the mixed layer base and the lower N 2 maximum (0.4 × 10 −4 s −2 ) is found at about 200 m depth in the eddy centre. The eddy core shows a constant slope in temperature/salinity (T /S) characteristic over the 2 months, but an erosion of the core progressively narrows down the T /S range. The eddy minimal oxygen concentrations decreased by about 5 µmol kg −1 in 2 months, confirming earlier estimates of oxygen consumption rates in these eddies. Separating the mesoscale and perturbation flow components reveals oscillating velocity finestructure (∼ 0.1 m s −1 ) underneath the eddy and at its flanks. The velocity finestrucure is organized in layers that align with layers in properties (salinity, temperature) but mostly cross through surfaces of constant density. The largest magnitude in velocity finestructure is seen between the surface and 140 m just outside the maximum mesoscale flow but also in a layer underneath the eddy centre, between 250 and 450 m. For both regions a cyclonic rotation of the velocity finestructure with depth suggests the vertical propagation of near-inertial wave (NIW) energy. Modification of the planetary vorticity by anticyclonic (eddy core) and cyclonic (eddy periphery) relative vorticity is most likely impacting the NIW energy propagation. Below the low oxygen core salt-finger type double diffusive layers are found that align with the velocity finestructure. Apparent oxygen utilization (AOU) versus dissolved inorganic nitrate (NO − 3 ) ratios are about twice as high (16) in the eddy core compared to surrounding waters (8.1). A large NO − 3 deficit of 4 to 6 µmol kg −1 is determined, rendering denitrification an unlikely explanation. Here it is hypothesized that the differences in local recycling of nitrogen and oxygen, as a result of the eddy dynamics, cause the shift in the AOU : NO sup>− 3 ratio. High NO − 3 and low oxygen waters are eroded by mixing from the eddy core and entrain into the mixed layer. The nitrogen is reintroduced into the core by gravitational settling of particulate matter out of the euphotic zone. The low oxygen water equilibrates in the mixed layer by air–sea gas exchange and does not participate in the gravitational sinking. Finally we propose a mesoscale–submesoscale interaction concept where wind energy, mediated via NIWs, drives nutrient supply to the euphotic zone and drives extraordinary blooms in anticyclonic mode-water eddies.
Constitutive IDO1 Expression in Human Tumors Is Driven by Cyclooxygenase-2 and Mediates Intrinsic Immune Resistance

Certain tumors resistant to immunotherapy express indoleamine 2,3-dioxygenase 1 (IDO1), due to oncogenic PI3K and MAPK signaling triggering autocrine prostaglandin secretion. Treatment with a COX-2 inhibitor reduced IDO1 expression and improved efficacy of immunotherapy. Tumors use various mechanisms to avoid immune destruction. Cyclooxygenase-2 (COX-2) expression may be a driver of immune suppression in melanoma, but the mechanisms involved remain elusive. Here, we show that COX-2 expression drives constitutive expression of indoleamine 2,3-dioxygenase 1 (IDO1) in human tumor cells. IDO1 is an immunosuppressive enzyme that degrades tryptophan. In a series of seven human tumor lines, constitutive IDO1 expression depends on COX-2 and prostaglandin E2 (PGE2), which, upon autocrine signaling through the EP receptor, activates IDO1 via the PKC and PI3K pathways. COX-2 expression itself depends on the MAPK pathway, which therefore indirectly controls IDO1 expression. Most of these tumors carry PI3K or MAPK oncogenic mutations, which may favor constitutive IDO1 expression. Celecoxib treatment promoted immune rejection of IDO1-expressing human tumor xenografts in immunodeficient mice reconstituted with human allogeneic lymphocytes. This effect was associated with a reduced expression of IDO1 in those ovarian SKOV3 tumors and an increased infiltration of CD3+ and CD8+ cells. Our results highlight the role of COX-2 in constitutive IDO1 expression by human tumors and substantiate the use of COX-2 inhibitors to improve the efficacy of cancer immunotherapy, by reducing constitutive IDO1 expression, which contributes to the lack of T-cell infiltration in “cold” tumors, which fail to respond to immunotherapy. Cancer Immunol Res; 5(8); 695–709. ©2017 AACR.
Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov

Background Photosynthetic eukaryotes with a secondary plastid of red algal origin (cryptophytes, haptophytes, stramenopiles, dinoflagellates, and apicomplexans) are hypothesized to share a single origin of plastid acquisition according to Chromalveolate hypothesis. Recent phylogenomic analyses suggest that photosynthetic “chromalveolates” form a large clade with inclusion of several non-photosynthetic protist lineages. Katablepharids are one such non-photosynthetic lineage closely related to cryptophytes. Despite their evolutionary and ecological importance, katablepharids are poorly investigated. Methodology/Principal Findings Here, we report a newly discovered flagellate, Roombia truncata gen. et sp. nov., that is related to katablepharids, but is morphologically distinct from othermembers of the group in the following ways: (1) two flagella emerge from a papilla-like subapical protrusion, (2) conspicuous ejectisomes are aligned in multiple (5–11) rows, (3) each ejectisome increases in size towards the posterior end of the rows, and (4) upon feeding, a part of cytoplasm elastically stretch to engulf whole prey cell. Molecular phylogenies inferred from Hsp90, SSU rDNA, and LSU rDNA sequences consistently and strongly show R. truncata as the sister lineage to all other katablepharids, including lineages known only from environmental sequence surveys. A close association between katablepharids and cryptophytes was also recovered in most analyses. Katablepharids and cryptophytes are together part of a larger, more inclusive, group that also contains haptophytes, telonemids, centrohelids and perhaps biliphytes. The monophyly of this group is supported by several different molecular phylogenetic datasets and one shared lateral gene transfer; therefore, we formally establish this diverse clade as the “Hacrobia. ” Conclusions/Significance Our discovery of R. truncata not only expands our knowledge in the less studied flagellate group, but provide a better understanding of phylogenetic relationship and evolutionary view of plastid acquisition/losses of Hacrobia. Being an ancestral to all katablepharids, and readily cultivable, R. truncata is a good candidate for multiple gene analyses that will contribute to future phylogenetic studies of Hacrobia.
Cycloplegic Refraction in Hyperopic Children: Effectiveness of a 0.5% Tropicamide and 0.5% Phenylephrine Addition to 1% Cyclopentolate Regimen

Purpose To evaluate the effectiveness of a cycloplegic regimen using 0.5% tropicamide and 0.5% phenylephrine (Tropherine, Hanmi Pharm), in addition to 1% cyclopentolate, in hyperopic children. Methods The medical records of hyperopic patients below the age of 14 years who had undergone cycloplegic retinoscopy were retrospectively reviewed. Cycloplegic refractions were performed using one of two cycloplegic regimens. Regimen 1 was a Tropherine-added regimen comprising the administration of one drop of 1% cyclopentolate followed by two to three drops of Tropherine added at 15-minute intervals. Regimen 2 was a cyclopentolate-only regimen comprising the administration of three to four drops of 1% cyclopentolate at 15-minute intervals. The mean difference between noncycloplegic and cycloplegic refraction was compared between the two regimens. Results A total of 308 eyes of 308 hyperopic children were included. The mean difference (±standard deviation) in the spherical equivalent (SE) between cycloplegic and noncycloplegic refraction was significantly larger in regimen 2 than in regimen 1, with values of +1.70 ± 1.03 diopters (D) and +1.25 ± 0.89 D, respectively (p=0.001). The SE change after cycloplegia was significantly different between the two regimens only in patients aged 5 years or younger (p=0.001), particularly in those with high hyperopia with an SE ≥5 D (p=0.005) or fully accommodative esotropia (p=0.009). There was no significant difference between the two regimens in patients older than 5 years, regardless of the presence of high hyperopia or fully accommodative esotropia. Conclusions The Tropherine-added regimen exerted a weaker cycloplegic effect than the cyclopentolate-only regimen, particularly in children under the age of 5 years with high hyperopia or fully accommodative esotropia. However, the difference in refraction between the two regimens was small. A Tropherine-added regimen can be effective in hyperopic children, with less associated discomfort than the instillation of cyclopentolate.