Miracle-dz/UniFAR-FTUs huggingface dataset:
An exhaustive inventory of coniferous trees in an agricultural landscape

Abstract Background Various species of forest trees are commonly used for ornamental purposes and are therefore frequently found in non-forest ecosystems. These trees constitute a significant component of the trees outside forests (TOF). Although increasingly recognized as prominent feature of agricultural lands and built-up areas, not much is known, however, about TOF since they are generally absent from forest inventories. New information In the present study, we focus on the coniferous tree species that constitute potential hosts for a forest defoliator, the pine processionary moth Thaumetopoea pityocampa Den. & Schiff. (Lepidoptera, Notodontidae). We carried out an exhaustive inventory of all pines (Pinus spp.), cedars (Cedrus spp.) and Douglas-fir (Pseudotsuga menziesii) in a 22 × 22 km study window located in the open-field region of Beauce in the centre of France. We recorded a total of 3834 individuals or small groups host trees corresponding a density of 7.9 occurrences per 100 ha. We provide the spatial coordinates of the points without differentiation between tree species.
An algebraic model for free rational G-spectra for connected compact Lie groups G

We show that the category of free rational G-spectra for a connected compact Lie group G is Quillen equivalent to the category of torsion differential graded modules over the polynomial ring H*(BG). The ingredients are the enriched Morita equivalences of Schwede and Shipley (Topology 42(1):103–153, 2003), the functors of Shipley (Am J Math 129:351–379, 2007) making rational spectra algebraic, Koszul duality and thick subcategory arguments based on the simplicity of the derived category of a polynomial ring.
Spoiling of transverse magnetization in gradient‐echo (GRE) imaging during the approach to steady state

The signal evolution behaviors and corresponding image appearances for different methods of spoiling or refocusing the transverse magnetization in short TR gradient‐echo imaging during the approach to steady state were investigated experimentally and using computer simulations based on the Bloch equations. Specifically, ideally spoiled, gradient‐spoiled, gradient‐refocused, and RF‐spoiled pulse sequence configurations were studied. This study showed that, for the gradient‐spoiled configuration, the signal evolution is position and phase‐encoding order‐dependent and, under typical imaging conditions, can deviate substantially from the ideally spoiled signal evolution at some spatial positions, resulting in intensity banding image artifacts. For the gradient‐refocused configuration, the signal evolution oscillates toward the steady state and, generally, does not closely approximate that of ideal spoiling, resulting in different image contrast or image blurring. Using RF spoiling, the signal evolution closely approximates the ideally spoiled case for flip angles less than approximately 20° and T2 values of less than approximately 200 ms and results in relatively artifact‐free images. Also, this study showed that, for RF spoiling, an RF‐pulse phase‐difference increment other than 117°, such as 84°, may be optimal for gradient‐echo imaging during the approach to steady state.
Clinical practice guidelines for the management of hypothyroidism.

INTRODUCTION Hypothyroidism has long been known for its effects on different organ systems, leading to hypometabolism. However, subclinical hypothyroidism, its most prevalent form, has been recently related to cardiovascular risk and also to maternal-fetal complications in pregnant women. OBJECTIVES In these clinical practice guidelines, several aspects of this field have been discussed with the clear objectives of helping physicians treat patients with hypothyroidism, and of sharing some of our Latin American-based clinical experience. MATERIALS AND METHODS The Latin American Thyroid Society commissioned a Task Force on Hypothyroidism to develop evidence-based clinical guidelines on hypothyroidism. A systematic review of the available literature, focused on the primary databases of MedLine/PubMed and Lilacs/SciELO was performed. Filters to assess methodological quality were applied to select the best quality studies. The strength of recommendation on a scale from A-D was based on the Oxford Centre for Evidence--based Medicine, Levels of Evidence 2009, allowing an unbiased opinion devoid of subjective viewpoints. The areas of interest for the studies comprised diagnosis, screening, treatment and a special section for hypothyroidism in pregnancy. RESULTS Several questions based on diagnosis, screening, treatment of hypothyroidism in adult population and specifically in pregnant women were posed. Twenty six recommendations were created based on the answers to these questions. Despite the fact that evidence in some areas of hypothyroidism, such as therapy, is lacking, out of 279 references, 73% were Grade A and B, 8% Grade C and 19% Grade D. CONCLUSIONS These evidence-based clinical guidelines on hypothyroidism will provide unified criteria for management of hypothyroidism throughout Latin America. Although most of the studies referred to are from all over the world, the point of view of thyroidologists from Latin America is also given.
An ontology of 3 D visualization techniques for enriched 3 D city models

Models, which represent in 3 dimensions the geometric elements of a city, are called 3D city models. Those models are used for an intended wide range of applications beyond mere visualization. Such uses are made possible by enriching the geometrical aspects with urban or environmental data that cannot be perceptible to a user without a visual abstraction. Using such models implies interacting with them in order to perform specific tasks related to the visualized data. Those data are potentially heterogeneous in terms of types, scales, issues, etc. When creating an enriched 3D city model, the designer faces the problem of choosing the most relevant visualization techniques for those heterogeneous data that have to be displayed within the same scene. In this paper we address the problem related to the visualization of enriched 3D city models by proposing a formal representation of existing visualization techniques in the form of an ontology of 3D visualization techniques. We also show how this ontology can be used for computational reasoning and help for the selection of visualization techniques by checking if a technique is compatible with a dataset to display or to a technique already selected and used in the same scene.
Imperatorin Inhibits HIV-1 Replication through an Sp1-dependent Pathway*

Coumarins and structurally related compounds have been recently shown to present anti-human immunodeficiency virus, type 1 (HIV-1) activity. Among them, the dietary furanocoumarin imperatorin is present in citrus fruits, in culinary herbs, and in some medicinal plants. In this study we report that imperatorin inhibits either vesicular stomatitis virus-pseudotyped or gp160-enveloped recombinant HIV-1 infection in several T cell lines and in HeLa cells. These recombinant viruses express luciferase as a marker of viral replication. Imperatorin did not inhibit the reverse transcription nor the integration steps in the viral cell cycle. Using several 5′ long terminal repeat-HIV-1 constructs where critical response elements were either deleted or mutated, we found that the transcription factor Sp1 is critical for the inhibitory activity of imperatorin induced by both phorbol 12-myristate 13-acetate and HIV-1 Tat. Moreover in transient transfections imperatorin specifically inhibited phorbol 12-myristate 13-acetate-induced transcriptional activity of the Gal4-Sp1 fusion protein. Since Sp1 is also implicated in cell cycle progression we further studied the effect of imperatorin on cyclin D1 gene transcription and protein expression and in HeLa cell cycle progression. We found that imperatorin strongly inhibited cyclin D1 expression and arrested the cells at the G1 phase of the cell cycle. These results highlight the potential of Sp1 transcription factor as a target for natural anti-HIV-1 compounds such as furanocoumarins that might have a potential therapeutic role in the management of AIDS.
Coordinate Discrete Optimization for Efficient Cross-View Image Retrieval

Learning compact hash codes has been a vibrant research topic for large-scale similarity search owing to the low storage cost and expedited search operation. A recent research thrust aims to learn compact codes jointly from multiple sources, referred to as cross-view (or cross-modal) hashing in the literature. The main theme of this paper is to develop a novel formulation and optimization scheme for cross-view hashing. As a key differentiator, our proposed method directly conducts optimization on discrete binary hash codes, rather than relaxed continuous variables as in existing cross-view hashing methods. This way relaxation-induced search accuracy loss can be avoided. We attack the crossview hashing problem by simultaneously capturing semantic neighboring relations and maximizing the generative probability of the learned hash codes in each view. Specifically, to enable effective optimization on discrete hash codes, the optimization proceeds in a block coordinate descent fashion. Each iteration sequentially updates a single bit with others clamped. We transform the resultant sub-problem into an equivalent, more tractable quadratic form and devise an active set based solver on the discrete codes. Rigorous theoretical analysis is provided for the convergence and local optimality condition. Comprehensive evaluations are conducted on three image benchmarks. The clearly superior experimental results faithfully prove the merits of the proposed method.
Nonviral genetic modification mediates effective transgene expression and functional RNA interference in human mesenchymal stem cells

Human mesenchymal stem cells (hMSC) are increasingly the focus of both basic and clinical research due to their ability to strike a balance between self‐renewal and commitment to mesodermal differentiation. However, the promising therapeutic utility of hMSC in regenerative medical approaches requires detailed knowledge about their molecular characteristics. Therefore, genetic modification of hMSC provides a powerful tool to understand their complex molecular regulation mechanisms.
Dynamic Oracle for Neural Machine Translation in Decoding Phase

The past several years have witnessed the rapid progress of end-to-end Neural Machine Translation (NMT). However, there exists discrepancy between training and inference in NMT when decoding, which may lead to serious problems since the model might be in a part of the state space it has never seen during training. To address the issue, Scheduled Sampling has been proposed. However, there are certain limitations in Scheduled Sampling and we propose two dynamic oracle-based methods to improve it. We manage to mitigate the discrepancy by changing the training process towards a less guided scheme and meanwhile aggregating the oracle's demonstrations. Experimental results show that the proposed approaches improve translation quality over standard NMT system.
A Buffer Management for STT-MRAM based Hybrid Main Memory in Sensor Nodes

As the power dissipation has become one of the critical design challenges in a sensor network environment, non- volatile memories such as STT-MRAM and flash memory will be used in the next generation sensor nodes. In this paper, we studied an efficient buffer management scheme considering the write limitation of STT-MRAM based main memory as well as the erase-before-write limitation of flash memory for storage device. The goal of proposed scheme is to minimize the number of write operations on STT- MRAM as well as the number of erase operations on flash memory. We showed through simulation that proposed scheme outperforms legacy buffer management schemes. Index Terms - Non-volatile memories, Low power, Buffer management, STT-MRAM, NAND flash memory.
Generalized Cost Analysis for Decentralized Search over Metric-embedded Networks

For this project, we consider the problem of routing messages between nodes in Small World [7] and related networks – i.e., networks that are embedded in some metric space, where the probability that a given edge is constructed is inversely proportional to the distance between its corresponding nodes. Our analysis differs from existing approaches in that we assume that each node in the network is assigned a priori some probability of failure independently from some underlying distribution, possibly identically for each node, or possibly from some family indexed by some property of the node (such as its degree). Given a sequence of random (source, target) pairs, we seek to minimize the total expected cost of routing a message from source to target over a fixed number of runs, where the cost is some function of path length and number of failures. We consider the aforementioned task in the context where each node failure rate is unknown, and each node v is given O(deg(v)) memory with which to estimate the failure rate of each of its neighbors. In this setting, we derive mathematical results about how to route using only local information, and we propose a number of strategies. We further test several of these strategies on synthetic data.
Asymptotic normality of nonparametric kernel type deconvolution density estimators: crossing the Cauchy boundary

We derive asymptotic normality of kernel type deconvolution density estimators. In particular, we consider deconvolution problems where the known component of the convolution has a symmetric λ-stable distribution with 0 < λ ≤ 2. It turns out that the limit behavior changes if the exponent parameter λ passes the value 1, the case of Cauchy deconvolution.
Genetics of Streptomyces rimosus, the Oxytetracycline Producer

SUMMARY From a genetic standpoint, Streptomyces rimosus is arguably the best-characterized industrial streptomycete as the producer of oxytetracycline and other tetracycline antibiotics. Although resistance to these antibiotics has reduced their clinical use in recent years, tetracyclines have an increasing role in the treatment of emerging infections and noninfective diseases. Procedures for in vivo and in vitro genetic manipulations in S. rimosus have been developed since the 1950s and applied to study the genetic instability of S. rimosus strains and for the molecular cloning and characterization of genes involved in oxytetracycline biosynthesis. Recent advances in the methodology of genome sequencing bring the realistic prospect of obtaining the genome sequence of S. rimosus in the near term.
Portfolio Choice and Corporate Financial Policy When There Are Tax-Intermediating Dealers

Miller (1977) emphasized that optimal corporate nancial policy depends on the tax rates facing the rm as well as the tax treatment accorded bond- and stock-holders. In equilibrium, rms will issue claims that are held by the full spectrum of investors, from tax-exempt institutional investors to heavily taxed individuals. However, dealers are tax neutral institutions that can buy corporate securities and, under some circumstances, reissue them as a nancial package with dieren t tax characteristics. This activity potentially severs the link between the securities the rm issues and the securities investors hold. In a continuous-time setting with dealers, I show that investors generally will hold derivatives, and possibly stock, in lieu of holding taxable bonds. Moreover, the marginal tax advantage to debt in this setting is the corporate tax rate.
CapnoBase: Signal database and tools to collect, share and annotate respiratory signals

Background and Objective The development of reliable and robust algorithms for the processing of biomedical signals in the operating room requires a series of high resolution signals recorded under different and known conditions. For algorithm tuning and validation, large datasets containing annotated clinical scenarios are required. These scenarios can be difficult to obtain, especially in the case of rare respiratory events recorded during anesthesia (e.g. rising end-tidal carbon dioxide (EtCO2) associated with malignant hyperthermia or anaphylaxis). The collection and annotation of data is very time consuming. In addition the comparative performance of an algorithm can only be assessed using a benchmark dataset. There is currently no public benchmarking dataset for respiratory signal analysis available. CapnoBase is a collaborative research project designed to provide easy to use research tools and a database of annotated respiratory signals including a benchmark dataset.
Emphysematous Gastritis Associated with Invasive Gastric Mucormycosis: A Case Report

Emphysematous gastritis is a rare form of phlegmonous gastritis, characterized by air in the wall of the stomach due to invasion by gas-forming microorganisms. The most commonly involved microorganisms are streptococci, Escherichia coli, Pseudomonas aeruginosa, Clostrodium perfrigens and Staphylococcus aureus. Gastrointestinal mucormycosis is another rare condition, which is most frequently occurs in the stomach. Because emphysematous gastritis associated with invasive gastric mucormycosis is an extremely rare clinical condition and both are life-threatening diseases, early precise diagnosis and early treatment should be done to avoid mortality. Herein we present an extremely rare case of emphysematous gastritis associated with invasive gastric mucormycosis. A 43-yr-old man, suffering from alcoholism and diabetes, has experienced diffuse abdominal pain for 4 days. Abdominal computed tomography scan demonstrated gas within the stomach wall. A histologic examination of the total gastrectomy specimen showed several gas-filled bubbles in the wall, along with numerous fungal hyphae throughout the necrotic stomach wall. He died of multiorgan failure secondary to disseminated mucormycosis, despite the intensive medical therapy.
The trace norm constrained matrix-variate Gaussian process for multitask bipartite ranking

We propose a novel hierarchical model for multitask bipartite ranking. The proposed approach combines a matrix-variate Gaussian process with a generative model for task-wise bipartite ranking. In addition, we employ a novel trace constrained variational inference approach to impose low rank structure on the posterior matrix-variate Gaussian process. The resulting posterior covariance function is derived in closed form, and the posterior mean function is the solution to a matrix-variate regression with a novel spectral elastic net regularizer. Further, we show that variational inference for the trace constrained matrix-variate Gaussian process combined with maximum likelihood parameter estimation for the bipartite ranking model is jointly convex. Our motivating application is the prioritization of candidate disease genes. The goal of this task is to aid the identification of unobserved associations between human genes and diseases using a small set of observed associations as well as kernels induced by gene-gene interaction networks and disease ontologies. Our experimental results illustrate the performance of the proposed model on real world datasets. Moreover, we find that the resulting low rank solution improves the computational scalability of training and testing as compared to baseline models.
Modeling the Chronotropic Effect of Isoprenaline on Rabbit Sinoatrial Node

Introduction: β-adrenergic stimulation increases the heart rate by accelerating the electrical activity of the pacemaker of the heart, the sinoatrial node (SAN). Ionic mechanisms underlying the actions of β-adrenergic stimulation are not yet fully understood. Isoprenaline (ISO), a β-adrenoceptor agonist, shifts voltage-dependent If activation to more positive potentials resulting in an increase of If, which has been suggested to be the main mechanism underlying the effect of β-adrenergic stimulation. However, ISO has been found to increase the firing rate of rabbit SAN cells when If is blocked. ISO also increases ICaL, Ist, IKr, and IKs; and shifts the activation of IKr to more negative potentials and increases the rate of its deactivation. ISO has also been reported to increase the intracellular Ca2+ transient, which can contribute to chronotropy by modulating the “Ca2+ clock. ” The aim of this study was to analyze the ionic mechanisms underlying the positive chronotropy of β-adrenergic stimulation using two distinct and well established computational models of the electrical activity of rabbit SAN cells. Methods and results: We modified the Boyett et al. (2001) and Kurata et al. (2008) models of electrical activity for the central and peripheral rabbit SAN cells by incorporating equations for the known dose-dependent actions of ISO on various ionic channel currents (ICaL, Ist, IKr, and IKs), kinetics of IKr and If, and the intracellular Ca2+ transient. These equations were constructed from experimental data. To investigate the ionic basis of the effects of ISO, we simulated the chronotropic effect of a range of ISO concentrations when ISO exerted all its actions or just a subset of them. Conclusion: In both the Boyett et al. and Kurata et al. SAN models, the chronotropic effect of ISO was found to result from an integrated action of ISO on ICaL, If, Ist, IKr, and IKs, among which an increase in the rate of deactivation of IKr plays a prominent role, though the effect of ISO on If and [Ca2+]i also plays a role.
Aspect-based Product Review Summarizer

Consumers are now relying on product reviews websites to aid them in deciding which product to buy. These sites contain large number of reviews and reading through them is tedious. In this work, we propose building a product review summarizer which will process all the reviews for a product and present them in an easy to read manner. The generated summaries show a list of product features or aspects and their corresponding rating, allowing users in comparing between different products easily. Our system first makes use of an aspect/sentiment extractor to extract the list of aspects and their sentiment words. Sentiment classification is then performed to obtain the polarity of aspects. Finally, these aspects are combined and assigned a rating to form the final summary. The experimental results on various domains have shown that our system is promising.
Synergistic effect of HIF-1α gene therapy and HIF-1-activated bone marrow-derived angiogenic cells in a mouse model of limb ischemia

Ischemia induces the production of angiogenic cytokines and the homing of bone-marrow-derived angiogenic cells (BMDACs), but these adaptive responses become impaired with aging because of reduced expression of hypoxia-inducible factor (HIF)-1α. In this study, we analyzed the effect of augmenting HIF-1α levels in ischemic limb by intramuscular injection of AdCA5, an adenovirus encoding a constitutively active form of HIF-1α, and intravenous administration of BMDACs that were cultured in the presence of the prolyl-4-hydroxylase inhibitor dimethyloxalylglycine (DMOG) to induce HIF-1 expression. The combined therapy increased perfusion, motor function, and limb salvage in old mice subjected to femoral artery ligation. Homing of BMDACs to the ischemic limb was dramatically enhanced by intramuscular AdCA5 administration. DMOG treatment of BMDACs increased cell surface expression of β2 integrins, which mediated increased adherence of BMDACs to endothelial cells. The effect of DMOG was abolished by coadministration of the HIF-1 inhibitor digoxin or by preincubation with a β2 integrin-blocking antibody. Transduction of BMDACs with lentivirus LvCA5 induced effects similar to DMOG treatment. Thus, HIF-1α gene therapy increases homing of BMDACs to ischemic muscle, whereas HIF-1 induction in BMDACs enhances their adhesion to vascular endothelium, leading to synergistic effects of combined therapy on tissue perfusion.