Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers

ABSTRACT The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms Oasisia alvinae, Riftia pachyptila, Tevnia jerichonana, and Ridgeia piscesae belong to the same phylotype of gammaproteobacteria, “Candidatus Endoriftia persephone. ” Comparisons of symbiont genomes between the East Pacific Rise tubeworms R. pachyptila and T. jerichonana confirmed that these two hosts share the same symbionts. Two Ridgeia symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced Riftia and Tevnia symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that “Ca. Endoriftia persephone” symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity. IMPORTANCE Remarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, “Candidatus Endoriftia persephone. ” Understanding the structure, dynamism, and interconnectivity of “Ca. Endoriftia persephone” populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species R. piscesae, from the Juan de Fuca Ridge. We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms R. pachyptila and T. jerichonana to develop a portrait of the “Ca. Endoriftia persephone” pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of “Ca. Endoriftia persephone” assemblies in the context of population genetics and molecular evolution.
Capturing CO2 from an integrated steel mill : a techno-economic analysis through process modelling

The increase in global carbon dioxide emission has raised concerns about climate change. This has caused nations to consider different carbon dioxide mitigation pathways to reduce emissions. The iron and steel industry contributes to approximately 30% of total global CO2 direct emission in the industrial sector. It is an energy intense industry. Many steel mills are operating close to thermodynamic limits in efficiency. Therefore decarbonising the steel industry through process improvements is limited. Breakthrough technologies such as carbon capture and storage (CCS) is an alternative and attractive solution. In this research I have explored the application of a retrofit carbon capture technology to an existing steel mill. The steel mill chosen, combusts gases arising from the steel making processes. Different locations within the steel mill were analysed, the in-house power station and the turbo blower house were chosen for retrofit post-combustion carbon capture. Two different separation technologies were process modelled to capture the carbon dioxide from the flue gas of the in-house power station and the turbo blower house. The technologies were chemical absorption and adsorption. The two technologies were techno-economically studied. Chemical absorption, with solvent MEA, showed capability of recovering 86% of CO2 with a purity of more than 99 mol%. Adsorption using sorbent zeolite 13X was able to achieve 82% recovery with purity of 96 mol%. Sorbent activated carbon showed a capability of recovering 67% of carbon dioxide with a purity of 95 mol%. The cost of CO2 avoidance for the process using chemical absorption (MEA) was equal to $44.92/tonne CO2. For the process using adsorption (zeolite 13X) the CO2 avoided cost was equal to $44.90/tonne of CO2. Activated carbon was the most expensive capture process, out of the three processes studied. It costs $45.81/tonne of CO2 avoidance.
A Randomized Trial of Cognitive Behavior Therapy and Cognitive Therapy for Children With Posttraumatic Stress Disorder Following Single-Incident Trauma: Predictors and Outcome at 1-Year Follow-Up

Objective: The 1-year outcome and moderators of adjustment for children and youth receiving treatment for posttraumatic stress disorder (PTSD) following single-incident trauma was examined. Method: Children and youth who had experienced single-incident trauma (N = 33; 7–17 years old) were randomly assigned to receive 9 weeks of either trauma-focused cognitive behavior therapy (CBT) or trauma-focused cognitive therapy (without exposure; CT) that was administered to them and their parents individually. Results: Intent-to-treat analyses demonstrated that both groups maintained posttreatment gains in PTSD, depression and general anxiety symptoms reductions at 1-year follow-up, with no children meeting criteria for PTSD. A large proportion of children showed good end-state functioning at follow-up (CBT: 65%; CT: 71%). Contrary to 6-month outcomes, maternal adjustment no longer moderated children’s outcome, nor did any other tested variables. Conclusion: The findings confirm the positive longer-term outcomes of using trauma-focused cognitive–behavioral methods for PTSD secondary to single-incident trauma and that these outcomes are not dependent on the use of exposure.
The Lovasz-Softmax Loss: A Tractable Surrogate for the Optimization of the Intersection-Over-Union Measure in Neural Networks

The Jaccard index, also referred to as the intersection-over-union score, is commonly employed in the evaluation of image segmentation results given its perceptual qualities, scale invariance - which lends appropriate relevance to small objects, and appropriate counting of false negatives, in comparison to per-pixel losses. We present a method for direct optimization of the mean intersection-over-union loss in neural networks, in the context of semantic image segmentation, based on the convex LovÃ¡sz extension of submodular losses. The loss is shown to perform better with respect to the Jaccard index measure than the traditionally used cross-entropy loss. We show quantitative and qualitative differences between optimizing the Jaccard index per image versus optimizing the Jaccard index taken over an entire dataset. We evaluate the impact of our method in a semantic segmentation pipeline and show substantially improved intersection-over-union segmentation scores on the Pascal VOC and Cityscapes datasets using state-of-the-art deep learning segmentation architectures.
Improvement in 24-hour bronchodilation and symptom control with aclidinium bromide versus tiotropium and placebo in symptomatic patients with COPD: post hoc analysis of a Phase IIIb study

Background A previous Phase IIIb study (NCT01462929) in patients with moderate to severe COPD demonstrated that 6 weeks of treatment with aclidinium led to improvements in 24-hour bronchodilation comparable to those with tiotropium, and improvement of symptoms versus placebo. This post hoc analysis was performed to assess the effect of treatment in the symptomatic patient group participating in the study. Methods Symptomatic patients (defined as those with Evaluating Respiratory Symptoms [E-RS™] in COPD baseline score ≥10 units) received aclidinium bromide 400 μg twice daily (BID), tiotropium 18 μg once daily (QD), or placebo, for 6 weeks. Lung function, COPD respiratory symptoms, and incidence of adverse events (AEs) were assessed. Results In all, 277 symptomatic patients were included in this post hoc analysis. Aclidinium and tiotropium treatment improved forced expiratory volume in 1 second (FEV1) from baseline to week 6 at all time points over 24 hours versus placebo. In addition, improvements in FEV1 from baseline during the nighttime period were observed for aclidinium versus tiotropium on day 1 (aclidinium 157 mL, tiotropium 67 mL; P<0.001) and week 6 (aclidinium 153 mL, tiotropium 90 mL; P<0.05). Aclidinium improved trough FEV1 from baseline versus placebo and tiotropium at day 1 (aclidinium 136 mL, tiotropium 68 mL; P<0.05) and week 6 (aclidinium 137 mL, tiotropium 71 mL; P<0.05). Aclidinium also improved early-morning and nighttime symptom severity, limitation of early-morning activities, and E-RS Total and domain scores versus tiotropium (except E-RS Chest Symptoms) and placebo over 6 weeks. Tolerability showed similar incidence of AEs in each arm. Conclusion In this post hoc analysis of symptomatic patients with moderate to severe COPD, aclidinium 400 μg BID provided additional improvements compared with tiotropium 18 μg QD in: 1) bronchodilation, particularly during the nighttime, 2) daily COPD symptoms (E-RS), 3) early-morning and nighttime symptoms, and 4) early-morning limitation of activity.
Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling

&NA; Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogenetics is the estimation of the marginal likelihood. This quantity is commonly used for comparing different evolutionary models, but its calculation, even for simple models, incurs high computational cost. Another interesting challenge relates to the estimation of the posterior distribution. Often, long Markov chains are required to get sufficient samples to carry out parameter inference, especially for tree distributions. In general, these problems are addressed separately by using different procedures. Nested sampling (NS) is a Bayesian computation algorithm, which provides the means to estimate marginal likelihoods together with their uncertainties, and to sample from the posterior distribution at no extra cost. The methods currently used in phylogenetics for marginal likelihood estimation lack in practicality due to their dependence on many tuning parameters and their inability of most implementations to provide a direct way to calculate the uncertainties associated with the estimates, unlike NS. In this article, we introduce NS to phylogenetics. Its performance is analysed under different scenarios and compared to established methods. We conclude that NS is a competitive and attractive algorithm for phylogenetic inference. An implementation is available as a package for BEAST 2 under the LGPL licence, accessible at https://github.com/BEAST2‐Dev/nested‐sampling.
Carbon Prices and Incentives for Technological Development

There is concern that the carbon prices generated through climate policies are too low to create the incentives necessary to stimulate technological development. This paper empirically analyzes how the Swedish carbon dioxide (CO2) tax and the European Union emission trading system (EU ETS) have affected productivity development in the Swedish pulp and paper industry 1998-2008. A Luenberger total factor productivity (TFP) indicator is computed using data envelopment analysis. The results show that climate policy had a modest impact on technological development in the pulp and paper industry, and if significant it was negative. The price of fossil fuels, on the contrary, seems to have created important incentives for technological development. Hence, the results suggest that the carbon prices faced by the industry through EU ETS and the CO2 tax have been too low. Even though the data for this study is specific for Sweden, the models and results are applicable internationally. When designing policy to mitigate CO2 emissions, it is vital that the policy creates a carbon price that is high enough - otherwise the pressure on technological development will not be sufficiently strong.
Changes in Muscle Architecture, Explosive Ability, and Track and Field Throwing Performance Throughout a Competitive Season and After a Taper

Abstract Bazyler, CD, Mizuguchi, S, Harrison, AP, Sato, K, Kavanaugh, AA, DeWeese, BH, and Stone, MH. Changes in muscle architecture, explosive ability, and track and field throwing performance throughout a competitive season and after a taper. J Strength Cond Res 31(10): 2785–2793, 2017—The purpose of this study was to examine the effects of an overreach and taper on measures of muscle architecture, jumping, and throwing performance in Division I collegiate throwers preparing for conference championships. Six collegiate track and field throwers (3 hammer, 2 discus, 1 javelin) trained for 12 weeks using a block-periodization model culminating with a 1-week overreach followed by a 3-week taper (ORT). Session rating of perceived exertion training load (RPETL) and strength training volume-load times bar displacement (VLd) were recorded weekly. Athletes were tested pre-ORT and post-ORT on measures of vastus lateralis architecture, unloaded and loaded squat and countermovement jump performance, underhand and overhead throwing performance, and competition throwing performance. There was a statistical reduction in weight training VLd/session (d = 1.21, p ⩽ 0.05) and RPETL/session (d = 0.9, p ⩽ 0.05) between the in-season and ORT training phases. Five of 6 athletes improved overhead throw and competition throwing performance after the ORT (d = 0.50, p ⩽ 0.05). Vastus lateralis muscle thickness statistically increased after the in-season training phase (d = 0.28, p ⩽ 0.05) but did not change after the ORT. Unloaded countermovement jump peak force and relative peak power improved significantly after the ORT (d = 0.59, p ⩽ 0.05, d = 0.31, p ⩽ 0.05, respectively). These findings demonstrate that an overreaching week followed by a 3-week taper is an effective means of improving explosive ability and throwing performance in collegiate track and field throwers despite the absence of detectable changes in muscle architecture.
SALT: Provably good routing topology by a novel steiner shallow-light tree algorithm

In a weighted undirected graph, a spanning/Steiner shallow-light tree (SLT) simultaneously approximates (i) shortest distances from a root to the other vertices, and (ii) the minimum tree weight. The Steiner SLT has been proved to be exponentially lighter than the spanning one [1], [2]. In this paper, we propose a novel Steiner SLT construction method called SALT (Steiner shAllow-Light Tree), which is efficient and has the tightest bound over all the state-of-the-art SLT algorithms. Applying SALT to Manhattan space offers a smooth trade-off between rectilinear Steiner minimum tree (RSMT) and rectilinear Steiner minimum arborescence (RSMA) for VLSI routing. In addition, the adaption further reduces the time complexity from O(n2) to O(n log n). The experimental results show that SALT can achieve not only short path lengths and wirelength but also small delay, compared to both classical and recent routing tree construction methods.
Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus

ABSTRACT We present the complete genome sequences of four members of a novel group of phages infecting Streptococcus thermophilus, designated here as the 987 group. Members of this phage group appear to have resulted from genetic exchange events, as evidenced by their “hybrid” genomic architecture, exhibiting DNA sequence relatedness to the morphogenesis modules of certain P335 group Lactococcus lactis phages and to the replication modules of S. thermophilus phages. All four identified members of the 987 phage group were shown to elicit adsorption affinity to both their cognate S. thermophilus hosts and a particular L. lactis starter strain. The receptor binding protein of one of these phages (as a representative of this novel group) was defined using an adsorption inhibition assay. The emergence of a novel phage group infecting S. thermophilus highlights the continuous need for phage monitoring and development of new phage control measures. IMPORTANCE Phage predation of S. thermophilus is an important issue for the dairy industry, where viral contamination can lead to fermentation inefficiency or complete fermentation failure. Genome information and phage-host interaction studies of S. thermophilus phages, particularly those emerging in the marketplace, are an important part of limiting the detrimental impact of these viruses in the dairy environment.
Regularizing RNNs for Caption Generation by Reconstructing the Past with the Present

Recently, caption generation with an encoder-decoder framework has been extensively studied and applied in different domains, such as image captioning, code captioning, and so on. In this paper, we propose a novel architecture, namely Auto-Reconstructor Network (ARNet), which, coupling with the conventional encoder-decoder framework, works in an end-to-end fashion to generate captions. ARNet aims at reconstructing the previous hidden state with the present one, besides behaving as the input-dependent transition operator. Therefore, ARNet encourages the current hidden state to embed more information from the previous one, which can help regularize the transition dynamics of recurrent neural networks (RNNs). Extensive experimental results show that our proposed ARNet boosts the performance over the existing encoder-decoder models on both image captioning and source code captioning tasks. Additionally, ARNet remarkably reduces the discrepancy between training and inference processes for caption generation. Furthermore, the performance on permuted sequential MNIST demonstrates that ARNet can effectively regularize RNN, especially on modeling long-term dependencies. Our code is available at: https://github.com/chenxinpeng/ARNet.
The Popular Roommates problem

We consider the popular matching problem in a roommates instance with strict preference lists. While popular matchings always exist in a bipartite instance, they need not exist in a roommates instance. The complexity of the popular matching problem in a roommates instance has been an open problem for several years and here we show it is NP-hard. A sub-class of max-size popular matchings called dominant matchings has been well-studied in bipartite graphs. We show that the dominant matching problem in a roommates instance is also NP-hard and this is the case even when the instance admits a stable matching.
Tropospheric ozonesonde profiles at long‐term U.S. monitoring sites: 2. Links between Trinidad Head, CA, profile clusters and inland surface ozone measurements

Much attention has been focused on the transport of ozone (O3) to the western U.S., particularly given the latest revision of the National Ambient Air Quality Standard to 70 parts per billion by volume (ppbv) of O3. This makes quantifying the contributions of stratosphere‐to‐troposphere exchange, local pollution, and pollution transport to this region essential. To evaluate free‐tropospheric and surface O3 in the western U.S., we use self‐organizing maps to cluster 18 years of ozonesonde profiles from Trinidad Head, CA. Three of nine O3 mixing ratio profile clusters exhibit thin laminae of high O3 above Trinidad Head. The high O3 layers are located between 1 and 6 km above mean sea level and reside above an inversion associated with a northern location of the Pacific subtropical high. Ancillary data (reanalyses, trajectories, and remotely sensed carbon monoxide) help identify the high O3 sources in one cluster, but distinguishing mixed influences on the elevated O3 in other clusters is difficult. Correlations between the elevated tropospheric O3 and surface O3 at high‐altitude monitors at Lassen Volcanic and Yosemite National Parks, and Truckee, CA, are marked and long lasting. The temporal correlations likely result from a combination of transport of baseline O3 and covarying meteorological parameters. Days corresponding to the high O3 clusters exhibit hourly surface O3 anomalies of +5–10 ppbv compared to a climatology; the positive anomalies can last up to 3 days after the ozonesonde profile. The profile and surface O3 links demonstrate the importance of regular ozonesonde profiling at Trinidad Head.
Photometric Stereo in Participating Media Considering Shape-Dependent Forward Scatter

Images captured in participating media such as murky water, fog, or smoke are degraded by scattered light. Thus, the use of traditional three-dimensional (3D) reconstruction techniques in such environments is difficult. In this paper, we propose a photometric stereo method for participating media. The proposed method differs from previous studies with respect to modeling shape-dependent forward scatter. In the proposed model, forward scatter is described as an analytical form using lookup tables and is represented by spatially-variant kernels. We also propose an approximation of a large-scale dense matrix as a sparse matrix, which enables the removal of forward scatter. Experiments with real and synthesized data demonstrate that the proposed method improves 3D reconstruction in participating media.
The role of cementation in the behaviour of cemented soils

The behaviour of cemented soil and the role of cementation are reviewed based on experimental results. The review is presented in terms of geomechanics concepts in which the cemented soil may be modelled by elasticity and hardening plasticity concepts. No modelling equations are given, but the observed behaviour is analysed in view of the components entering into an elastoplastic model. These consist of an elastic range in stress space in which energy is not created or expended, a cementation yield surface, a 3D failure surface, a plastic potential, a yield surface and the associated plastic hardening law.
Durable response to bevacizumab in adults with recurrent pilocytic astrocytoma

Background: Adult pilocytic astrocytomas are rare and highly vascular tumors. Aim: We hypothesized that they may be uniquely responsive to bevacizumab (BEV). Patients: We present four adult patients with pathologically diagnosed WHO grade I pilocytic astrocytoma who had robust and durable responses to BEV at time of recurrence. Three patients developed radiographic changes on MRI, consistent with progressive disease based on response assessment in neuro-oncology criteria. Median time to recurrence was 8.5 months. Methods: All patients were treated with six cycles of BEV for recurrence. Results: At the end of treatment, all patients had achieved a clinical and radiographic response. Median follow-up time after BEV is 20.5 months. Conclusion: This suggests that BEV may have true antitumor activity in adult pilocytic astrocytomas and may be important for achieving durable disease control.